Describe the bug

After migrating to newest Vite (Rolldown based), following config works improperly on Windows:

import { defineConfig } from 'vite';

export default defineConfig({
  build: {
    ssr: true,
    ssrEmitAssets: true,
    rollupOptions: {
      input: ['src/bin/index.ts'],
      output: {
        preserveModules: true,
        preserveModulesRoot: 'src',
      },
    },
  },
});

Source structure:

src/
├─ bin/
│  ├─ index.ts
├─ lib/
│  ├─ helper.ts
assets/
├─ data.json

Output on Windows:

vite v8.0.14 building ssr environment for production...
✓ 4 modules transformed.
computing gzip size...
dist/assets/data.js     0.09 kB │ gzip: 0.09 kB
dist/src/lib/helper.js  0.12 kB │ gzip: 0.12 kB
dist/src/bin/index.js   0.19 kB │ gzip: 0.14 kB

Output on Linux (node:22.13 image):

vite v8.0.14 building ssr environment for production...
✓ 4 modules transformed.
computing gzip size...
dist/assets/data.js  0.09 kB │ gzip: 0.09 kB
dist/lib/helper.js   0.12 kB │ gzip: 0.12 kB
dist/bin/index.js    0.19 kB │ gzip: 0.14 kB

Seems to be similar to previously fixed #6509 but related to Rolldown.

Reproduction

https://stackblitz.com/edit/vitejs-vite-wybkjasr

Steps to reproduce

1. Work on Windows
2. Have file structure similar as above (src directory, and something outside of src)
3. In vite.config.ts, have defined ssr: true, preserveModules: true and preserveModulesRoot: 'src'
4. Run vite build and check generated output (dist layout)

System Info

System:
    OS: Windows 11 10.0.26200
    CPU: (12) x64 AMD Ryzen 5 PRO 5650U with Radeon Graphics     
    Memory: 7.45 GB / 30.83 GB
  Binaries:
    Node: 22.22.3 - C:\Program Files\nodejs\node.EXE
    npm: 10.9.8 - C:\Program Files\nodejs\npm.CMD
    pnpm: 9.6.0 - C:\Users\rawi\AppData\Local\pnpm\pnpm.EXE
  Browsers:
    Chrome: 148.0.7778.179
    Edge: Chromium (145.0.3800.97)
    Internet Explorer: 11.0.26100.8115
  npmPackages:
    vite: ^8.0.14 => 8.0.14

Used Package Manager

npm

Logs

No response

Validations

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• The provided reproduction is a minimal reproducible example of the bug.