Ok, the initial issue is now fixed. It's possible to have more than one atexit module instance, registered callbacks in one or the other module are all called as expected. I also wrote an unit test for that.

I also took the opportunity of this issue to modernize the C code base, fix a bug in test_atexit (no longer clear atexit callbacks, run tests in subprocesses), and enhance atexit._run_exitfuncs(): log all callback exceptions using sys.unraisablehook so it's possible to catch them using the hook.