I've talked with Pablo about this in person, and as advised opening the issue here now. 

I've discovered that forked processes do not honour atexit registrations. See the following example code:

from multiprocessing import Process, set_start_method
import time
import os
import atexit


def cleanup():
    print(f"cleanup {os.getpid()}")


atexit.register(cleanup)


def run():
    time.sleep(0.1)
    print(f"process done {os.getpid()}")
    # atexit._run_exitfuncs()


if __name__ == "__main__":
    set_start_method("fork")
    process = Process(target=run)
    process.start()
    process.join()
    print("app finished")

In case of a forked process childs the atexit is never executed (note it works if I ran them manually at the end of the child process; so they're registered correctly). Switching to spawn method makes it work as expected. The behaviour is the same even if you call register within the child process (as opposed to being inherited during forking). Also found this StackOverflow question that mentions this https://stackoverflow.com/a/26476585. At the very least the documentation should explain this; though I'd expect atexit to be called before finalization of the fork processes (assuming the child process exits with 0 exit code). d