Reproduction link or steps

https://stackblitz.com/edit/github-vwaxybzu?file=src%2Ftest.js,rolldown.config.mjs

1. set up an output array with 2+ build outputs
2. run the build
3. check how many times the console.log() in the plugin's transform is called

What is expected?

Code should only be transformed once: console.log should only be called once in the example.

What is actually happening?

Code is transformed once per output: console.log is called once per output in the example.

System Info

System:
    OS: Windows 11 10.0.26100
    CPU: (64) x64 AMD Ryzen Threadripper 3970X 32-Core Processor
    Memory: 10.66 GB / 31.88 GB
  Binaries:
    Node: 23.5.0 - C:\Program Files\nodejs\node.EXE
    npm: 11.0.0 - C:\Program Files\nodejs\npm.CMD
  Browsers:
    Edge: Chromium (131.0.2903.99)
    Internet Explorer: 11.0.26100.1882
  npmPackages:
    rolldown: ^1.0.0-beta.1 => 1.0.0-beta.1

Any additional comments?

Rollup does not have this issue: there are no additional transform runs for example. There is only 1 full build.

Rolldown seems to be doing 1 full build per output item, which slows it down.

This is a follow-up to #3200