--registry parameter is not effective,when .modules.yaml exist

[wszgrcy]

Verify latest release

• I verified that the issue exists in the latest pnpm release

pnpm version

No response

Which area(s) of pnpm are affected? (leave empty if unsure)

CLI, Lockfile, Package manager compatibility

Link to the code that reproduces this issue or a replay of the bug

No response

Reproduction steps

// success
pnpm i lodash
//error
pnpm install my-private-repo   --registry=http://127.0.0.1:5555  -D

throw error

 ERR_PNPM_FETCH_404  GET https://registry.npmjs.org/my-private-repo: Not Found - 404

This error happened while installing a direct dependency of /home/user/my-project/adfs

my-private-repo is not in the npm registry, or you have no permission to fetch it.

An authorization header was used: Bearer npm_[hidden]
Progress: resolved 1, reused 1, downloaded 0, added 0

if I install my-private-repo first(without node_modules exist),It will install success

Describe the Bug

I think node_modules/.modules.yaml file save registries and then --registry not work

Expected Behavior

This operation can be successfully executed on NPM, so I hope it can also be compatible

Which Node.js version are you using?

20.10.0

Which operating systems have you used?

• macOS
• Windows
• Linux

If your OS is a Linux based, which one it is? (Include the version if relevant)

Ubuntu 22

[hjhcos]

pnpm service not use