bazel: bzlmod + build_python_zip breaks runfiles resolution

Description of the bug:

When building a py_binary with --build_python_zip and bzlmod enabled, the runfiles cannot be correctly resolved. Things would work if I remove the --build_python_zip option or switch back to the old WORKSPACE style. I suspect this has something to do with the way bzlmod handle repo mapping.

What’s the simplest, easiest way to reproduce this bug? Please provide a minimal example if possible.

I have a very small example to reproduce the issue: https://github.com/coquelicot/broken-bzlmod-pyzip

Here’s the log from my machine:

 » bazel run example
INFO: Build option --build_python_zip has changed, discarding analysis cache.
INFO: Analyzed target //:example (0 packages loaded, 539 targets configured).
INFO: Found 1 target...
Target //:example up-to-date:
  bazel-bin/example
INFO: Elapsed time: 0.280s, Critical Path: 0.01s
INFO: 4 processes: 4 internal.
INFO: Build completed successfully, 4 total actions
INFO: Running command line: bazel-bin/example
sample

 » bazel run --build_python_zip example
INFO: Build option --build_python_zip has changed, discarding analysis cache.
INFO: Analyzed target //:example (0 packages loaded, 539 targets configured).
INFO: Found 1 target...
Target //:example up-to-date:
  bazel-bin/example
  bazel-bin/example.zip
INFO: Elapsed time: 0.274s, Critical Path: 0.01s
INFO: 4 processes: 3 internal, 1 linux-sandbox.
INFO: Build completed successfully, 4 total actions
INFO: Running command line: bazel-bin/example
Traceback (most recent call last):
  File "/tmp/Bazel.runfiles_tuww8rqk/runfiles/_main/example.py", line 11, in <module>
    main()
  File "/tmp/Bazel.runfiles_tuww8rqk/runfiles/_main/example.py", line 6, in main
    with open(path, "r") as fin:
FileNotFoundError: [Errno 2] No such file or directory: '/tmp/Bazel.runfiles_tuww8rqk/runfiles/pyzip/data.txt'

Which operating system are you running Bazel on?

linux

What is the output of bazel info release?

release 6.1.1

If bazel info release returns development version or (@non-git), tell us how you built Bazel.

No response

What’s the output of git remote get-url origin; git rev-parse master; git rev-parse HEAD ?

No response

Have you found anything relevant by searching the web?

The way runfiles are implemented seems to be different with bzlmod: https://github.com/bazelbuild/bazel/issues/16124

Any other information, logs, or outputs that you want to share?

No response