dart doc mentions:

To generate documentation, you must first run dart pub get and your package must pass dart analyze without errors.

And dartdoc also mentions:

You must first run dart pub get or flutter pub get

I overlooked this information. However, even without flutter pub get the documentation was still fully functional, so I did not notice until git pull did not work anymore.

Now the GitHub runner generates the same files as my local device. The filenames are still equivalent to their corresponding source code paths but the name contains only the subpath below lib.