Automocking silently breaks with isolate: false + mixed mock types and resolve aliases #10145

Describe the bug

When isolate: false is set and two test files mock the same module differently, one with a factory (vi.mock(import('...'), () => (...))) and one with automocking (vi.mock(import('...'))), the automock is silently skipped if the factory-mock file runs first. The automocked module's exports are not replaced with vi.fn(), causing vi.mocked(fn).mockReturnValue(...) to throw:

TypeError: vi.mocked(...).mockReturnValue is not a function

The failure is intermittent because it depends on which test file runs first in the worker.

I believe a resolve.alias (e.g. ~ --> ./src) is required to trigger the bug because it causes the URL-based and ID-based registry keys to diverge (this particular diagnosis comes from Opus reviewing the commit that introduced the issue, I'm not necessarily sure enough myself)

This appears to be a regression between 4.1.0-beta.5 and 4.1.0-beta.6, and is still present in the latest versions.

Reproduction

https://github.com/kade-robertson/vitest-mock-isolate-repro

There are Github Action results on that repo you can inspect which runs the same test suite multiple times in vitest 4.1.0-beta.5 and 4.1.4. If you want to clone and run locally, pnpm install, and then run pnpm test:bad to run against 4.1.4 and pnpm test:good to run against 4.1.0-beta.5.

Note: This is a distilled reproduction as I'm not able to share the original test suite that caused this. This was done primarily with AI assistance, so some of the writing or contents of the README may be misleading.

System Info

System:
    OS: macOS 26.4
    CPU: (14) arm64 Apple M4 Pro
    Memory: 611.28 MB / 24.00 GB
    Shell: 4.6.0 - /opt/homebrew/bin/fish
  Binaries:
    Node: 24.13.0 - /Users/kade-mi/.local/share/mise/installs/node/24.13.0/bin/node
    npm: 11.6.2 - /Users/kade-mi/.local/share/mise/installs/node/24.13.0/bin/npm
    pnpm: 10.28.0 - /Users/kade-mi/.local/share/mise/installs/node/24.13.0/bin/pnpm
    Deno: 2.7.12 - /opt/homebrew/bin/deno
  Browsers:
    Chrome: 147.0.7727.56
    Chrome Canary: 148.0.7757.0
    Firefox: 147.0.3
    Firefox Developer Edition: 141.0
    Safari: 26.4
    Safari Technology Preview: 26.0
  npmPackages:
    @vitejs/plugin-react: 6.0.1 => 6.0.1
    @vitest/browser: 4.1.4 => 4.1.4
    @vitest/browser-playwright: 4.1.4 => 4.1.4
    @vitest/coverage-v8: 4.1.4 => 4.1.4
    @vitest/ui: 4.1.4 => 4.1.4
    playwright: 1.59.1 => 1.59.1
    vite: 8.0.8 => 8.0.8
    vitest: 4.1.4 => 4.1.4
    vitest-browser-react: 2.2.0 => 2.2.0

Used Package Manager

pnpm

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