This is so bizarre, as if fixing a config write to be atomic would somehow fix the root issue of this program was not designed with a config store in mind that

This is so bizarre, as if fixing a config write to be atomic would somehow fix the root issue of this program was not designed with a config store in mind that can tolerate multiple instances of itself. Because of course it doesn't. Because having multiple instances in parallel was a novel requirement you introduced that the original author obviously didn't care for. This isn't a learning experience about flock at all.