We switched to flit to make it easier for packagers (in particular Gentoo) to build the project. But my understanding at the time (2022) was that other packagers still depended on setup.py, so I left it in. Do you have a sense for how that ecosystem has evolved?

As far as I'm aware all major build frontends, mainly pip, poetry, uv, do support independent build systems now. So it should be safe to remove at this point.

Anecdotally, I've removed it on a number of other projects some time ago and so far I haven't seen any complains.