diff --git a/lib/config/defaults.ts b/lib/config/defaults.ts
index 1fd65e07b619c3..620d94c6d79efc 100644
--- a/lib/config/defaults.ts
+++ b/lib/config/defaults.ts
@@ -1,4 +1,4 @@
-import { getOptions } from './options';
+import { getOptions, isTopLevelOnlyOption } from './options';
 import type { AllConfig, RenovateOptions } from './types';
 
 // Use functions instead of direct values to avoid introducing global references.
@@ -23,7 +23,7 @@ export function getConfig(): AllConfig {
   const options = getOptions();
   const config: AllConfig = {};
   options.forEach((option) => {
-    if (!option.parents) {
+    if (!option.parents || isTopLevelOnlyOption(option)) {
       config[option.name] = getDefault(option);
     }
   });
diff --git a/lib/config/options/index.ts b/lib/config/options/index.ts
index 25131c290e21c8..49ddab51ffc160 100644
--- a/lib/config/options/index.ts
+++ b/lib/config/options/index.ts
@@ -210,6 +210,7 @@ const options: RenovateOptions[] = [
     experimentalDescription:
       'Config migration PRs are still being improved, in particular to reduce the amount of reordering and whitespace changes.',
     experimentalIssues: [16359],
+    parents: ['.'],
   },
   {
     name: 'productLinks',
@@ -269,6 +270,7 @@ const options: RenovateOptions[] = [
     subType: 'string',
     allowString: true,
     cli: false,
+    parents: ['.'],
   },
   {
     name: 'migratePresets',
@@ -401,6 +403,7 @@ const options: RenovateOptions[] = [
       'If enabled, Renovate logs the fully resolved config for each repository, plus the fully resolved presets.',
     type: 'boolean',
     default: false,
+    parents: ['.'],
   },
   {
     name: 'binarySource',
@@ -471,6 +474,7 @@ const options: RenovateOptions[] = [
     experimentalIssues: [23286],
     default: {},
     mergeable: true,
+    parents: ['.'],
   },
   {
     name: 'dockerChildPrefix',
@@ -580,6 +584,7 @@ const options: RenovateOptions[] = [
     type: 'string',
     allowedValues: ['auto', 'enabled', 'disabled'],
     default: 'auto',
+    parents: ['.'],
   },
   {
     name: 'includeMirrors',
@@ -686,6 +691,7 @@ const options: RenovateOptions[] = [
       'Whether to create a "Dependency Dashboard" issue in the repository.',
     type: 'boolean',
     default: false,
+    parents: ['.'],
   },
   {
     name: 'dependencyDashboardApproval',
@@ -700,12 +706,14 @@ const options: RenovateOptions[] = [
       'Set to `true` to let Renovate close the Dependency Dashboard issue if there are no more updates.',
     type: 'boolean',
     default: false,
+    parents: ['.'],
   },
   {
     name: 'dependencyDashboardTitle',
     description: 'Title for the Dependency Dashboard issue.',
     type: 'string',
     default: `Dependency Dashboard`,
+    parents: ['.'],
   },
   {
     name: 'dependencyDashboardHeader',
@@ -714,12 +722,14 @@ const options: RenovateOptions[] = [
     type: 'string',
     default:
       'This issue lists Renovate updates and detected dependencies. Read the [Dependency Dashboard](https://docs.renovatebot.com/key-concepts/dashboard/) docs to learn more.',
+    parents: ['.'],
   },
   {
     name: 'dependencyDashboardFooter',
     description:
       'Any text added here will be placed last in the Dependency Dashboard issue body, with a divider separator before it.',
     type: 'string',
+    parents: ['.'],
   },
   {
     name: 'dependencyDashboardLabels',
@@ -728,6 +738,7 @@ const options: RenovateOptions[] = [
     type: 'array',
     subType: 'string',
     default: null,
+    parents: ['.'],
   },
   {
     name: 'dependencyDashboardOSVVulnerabilitySummary',
@@ -737,6 +748,7 @@ const options: RenovateOptions[] = [
     allowedValues: ['none', 'all', 'unresolved'],
     default: 'none',
     experimental: true,
+    parents: ['.'],
   },
   {
     name: 'configWarningReuseIssue',
@@ -744,6 +756,7 @@ const options: RenovateOptions[] = [
       'Set this to `false` to make Renovate create a new issue for each config warning, instead of reopening or reusing an existing issue.',
     type: 'boolean',
     default: true,
+    parents: ['.'],
   },
 
   // encryption
@@ -1024,6 +1037,7 @@ const options: RenovateOptions[] = [
     subType: 'string',
     stage: 'package',
     cli: false,
+    parents: ['.'],
   },
   {
     name: 'useBaseBranchConfig',
@@ -1032,6 +1046,7 @@ const options: RenovateOptions[] = [
     type: 'string',
     allowedValues: ['merge', 'none'],
     default: 'none',
+    parents: ['.'],
   },
   {
     name: 'gitAuthor',
@@ -1071,6 +1086,7 @@ const options: RenovateOptions[] = [
     subType: 'string',
     mergeable: false,
     stage: 'repository',
+    parents: ['.'],
   },
   {
     name: 'includePaths',
@@ -1999,6 +2015,7 @@ const options: RenovateOptions[] = [
       'Rate limit PRs to maximum x created per hour. 0 means no limit.',
     type: 'integer',
     default: 2,
+    parents: ['.'],
   },
   {
     name: 'prConcurrentLimit',
@@ -2006,6 +2023,7 @@ const options: RenovateOptions[] = [
       'Limit to a maximum of x concurrent branches/PRs. 0 means no limit.',
     type: 'integer',
     default: 10,
+    parents: ['.'],
   },
   {
     name: 'branchConcurrentLimit',
@@ -2013,6 +2031,7 @@ const options: RenovateOptions[] = [
       'Limit to a maximum of x concurrent branches. 0 means no limit, `null` (default) inherits value from `prConcurrentLimit`.',
     type: 'integer',
     default: null, // inherit prConcurrentLimit
+    parents: ['.'],
   },
   {
     name: 'prPriority',
@@ -2111,6 +2130,7 @@ const options: RenovateOptions[] = [
     cli: false,
     env: false,
     supportedPlatforms: ['github'],
+    parents: ['.'],
   },
   {
     name: 'osvVulnerabilityAlerts',
@@ -2119,6 +2139,7 @@ const options: RenovateOptions[] = [
     default: false,
     experimental: true,
     experimentalIssues: [20542],
+    parents: ['.'],
   },
   {
     name: 'pruneBranchAfterAutomerge',
@@ -2266,6 +2287,7 @@ const options: RenovateOptions[] = [
     additionalProperties: {
       type: 'string',
     },
+    parents: ['.'],
   },
   {
     name: 'lockFileMaintenance',
@@ -2495,6 +2517,7 @@ const options: RenovateOptions[] = [
     stage: 'repository',
     cli: true,
     mergeable: true,
+    parents: ['.'],
   },
   {
     name: 'hostType',
@@ -2796,6 +2819,7 @@ const options: RenovateOptions[] = [
     stage: 'package',
     cli: true,
     mergeable: true,
+    parents: ['.'],
   },
   {
     name: 'customType',
@@ -3014,6 +3038,7 @@ const options: RenovateOptions[] = [
     experimental: true,
     globalOnly: true,
     default: [],
+    parents: ['.'],
   },
   {
     name: 'maxRetryAfter',
@@ -3034,6 +3059,7 @@ const options: RenovateOptions[] = [
     stage: 'repository',
     cli: false,
     env: false,
+    parents: ['.'],
   },
   {
     name: 'matchMessage',
@@ -3073,6 +3099,10 @@ export function getOptions(): RenovateOptions[] {
   return options;
 }
 
+export function isTopLevelOnlyOption(option: RenovateOptions): boolean {
+  return option.parents?.length === 1 && option.parents[0] === '.';
+}
+
 function loadManagerOptions(): void {
   const allManagers = new Map([...getManagers(), ...getCustomManagers()]);
   for (const [name, config] of allManagers.entries()) {
diff --git a/lib/config/types.ts b/lib/config/types.ts
index 2aa2cd155230eb..32f3ae9e0e429b 100644
--- a/lib/config/types.ts
+++ b/lib/config/types.ts
@@ -394,6 +394,7 @@ export interface ValidationMessage {
 }
 
 export type AllowedParents =
+  | '.' // Root
   | 'customManagers'
   | 'customDatasources'
   | 'hostRules'
diff --git a/lib/config/validation.ts b/lib/config/validation.ts
index 80f007f20a224a..b8b7864b51cf06 100644
--- a/lib/config/validation.ts
+++ b/lib/config/validation.ts
@@ -276,9 +276,13 @@ export async function validateConfig(
         !optionParents[key].includes(parentName as AllowedParents)
       ) {
         // TODO: types (#22198)
-        const message = `${key} should only be configured within one of "${optionParents[
+        let message = `${key} should only be configured within one of "${optionParents[
           key
         ]?.join(' or ')}" objects. Was found in ${parentName}`;
+        message = message.replace(
+          'within one of "." objects',
+          'at the top level',
+        );
         warnings.push({
           topic: `${parentPath ? `${parentPath}.` : ''}${key}`,
           message,
diff --git a/test/documentation.spec.ts b/test/documentation.spec.ts
index 6d1d54ce339926..2e053b30259c87 100644
--- a/test/documentation.spec.ts
+++ b/test/documentation.spec.ts
@@ -1,6 +1,6 @@
 import fs from 'fs-extra';
 import { glob } from 'glob';
-import { getOptions } from '../lib/config/options';
+import { getOptions, isTopLevelOnlyOption } from '../lib/config/options';
 import { regEx } from '../lib/util/regex';
 
 const options = getOptions();
@@ -29,7 +29,7 @@ describe('documentation', () => {
       function getRequiredConfigOptions(): string[] {
         return options
           .filter((option) => !option.globalOnly)
-          .filter((option) => !option.parents)
+          .filter((option) => !option.parents || isTopLevelOnlyOption(option))
           .filter((option) => !option.autogenerated)
           .map((option) => option.name)
           .sort();
@@ -59,7 +59,7 @@ describe('documentation', () => {
         return options
           .filter((option) => option.stage !== 'global')
           .filter((option) => !option.globalOnly)
-          .filter((option) => option.parents)
+          .filter((option) => option.parents && !isTopLevelOnlyOption(option))
           .map((option) => option.name)
           .sort();
       }
diff --git a/tools/docs/schema.ts b/tools/docs/schema.ts
index 293e713af91ba0..db1fc9b6fb8bbc 100644
--- a/tools/docs/schema.ts
+++ b/tools/docs/schema.ts
@@ -75,7 +75,7 @@ function createSingleConfig(option: RenovateOptions): Record<string, unknown> {
 
 function createSchemaForParentConfigs(): void {
   for (const option of options) {
-    if (!option.parents) {
+    if (!option.parents || option.parents.includes('.')) {
       properties[option.name] = createSingleConfig(option);
     }
   }
@@ -85,6 +85,9 @@ function addChildrenArrayInParents(): void {
   for (const option of options) {
     if (option.parents) {
       for (const parent of option.parents) {
+        if (parent === '.') {
+          continue;
+        }
         properties[parent].items = {
           allOf: [
             {
@@ -120,6 +123,9 @@ function createSchemaForChildConfigs(): void {
   for (const option of options) {
     if (option.parents) {
       for (const parent of option.parents) {
+        if (parent === '.') {
+          continue;
+        }
         properties[parent].items.allOf[0].properties[option.name] =
           createSingleConfig(option);
       }