Reproduction link or steps

1. Open https://stackblitz.com/edit/rolldown-rolldown-starter-stackblitz-vhbk3vhe?file=src%2Fentry.js
2. pnpm i runs automatically
3. pnpm build runs automatically

What is expected?

node dist/entry.js returns the same output with node src/entry.js.

[Module: null prototype] { default: 'foo' }

What is actually happening?

node dist/entry.js returns a different output from node src/entry.js.

[Module: null prototype] { }

System Info

StackBlitz

  System:
    OS: Linux 5.0 undefined
    CPU: (8) x64 Intel(R) Core(TM) i9-9880H CPU @ 2.30GHz
    Memory: 0 Bytes / 0 Bytes
    Shell: 1.0 - /bin/jsh
  Binaries:
    Node: 20.19.1 - /usr/local/bin/node
    Yarn: 1.22.19 - /usr/local/bin/yarn
    npm: 10.8.2 - /usr/local/bin/npm
    pnpm: 8.15.6 - /usr/local/bin/pnpm
  npmPackages:
    @rolldown/browser:  1.0.0-beta.13-commit.baedab7

Any additional comments?

I found this while testing preserveEntrySignatures: false with nuxt. I haven't traced down whether this is the reason why setting preserveEntrySignatures: false breaks nuxt, but I guess it is.

refs #3500 cc @IWANABETHATGUY