fix: revert ensure module in graph before transforming (#12774)

[dominikg]

This reverts commit 44ad321. #12774

Calling the moduleGraph and ensureWatchedFile early caused document requests to end up on the watchlist.
fixes #12926

Description

Additional context

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What is the purpose of this pull request?

• Bug fix
• New Feature
• Documentation update
• Other

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[patak-dev]

/ecosystem-ci run

[vite-ecosystem-ci]

📝 Ran ecosystem CI: Open

suite	result
astro	✅ success
histoire	✅ success
iles	✅ success
ladle	✅ success
laravel	✅ success
marko	✅ success
nuxt	✅ success
previewjs	✅ success
qwik	✅ success
rakkas	✅ success
sveltekit	✅ success
vite-plugin-ssr	✅ success
vite-plugin-react	❌ failure
vite-plugin-react-pages	✅ success
vite-plugin-react-swc	✅ success
vite-plugin-svelte	✅ success
vite-plugin-vue	✅ success
vite-setup-catalogue	✅ success
vitepress	✅ success
vitest	❌ failure
windicss	✅ success

[patak-dev]

Thanks for digging into this @dominikg!

Vitest and vite-plugin-react are also failing in main, so it is unrelated.

Let's revert for now and release a patch to close the regression. I still think that this change made sense so maybe we can re-apply it with a guard.