The comment makes it seem like having the file might impact operations. So having it would be a mistake

Exactly, having the file there is a mistake. It messes up namespace packages in the distributions we release. It's important that

src/python/pants/__init__.py

is not present. The risk with gitignoring it is that it's more likely you have the file without realizing. Whereas if you don't gitignore it, you will see the file is being added. For example,

release.sh

errors if the git state is not clean, so it won't allow it