Start with pythons “projectdirs”, which refuses to allow mac systems to use XDG or at least have that option.

https://github.com/platformdirs/platformdirs/issues/4

Do any of the Linux distros do this? Strikes me as the kind of thing Debian would do for everything in apt

Do you have any examples of Debian doing this?

Sure. In software of mine distributed by Debian, there's usually a "debian/patches" directory, that I didn't add, that's changes the Debian project wanted to make to the system. I'm sure there's a formal name for that system. Most Debian packages seem to have one.