Honestly it's a mess right now. The game used to fully support Xbox controllers on PC but it never supported non-Microsoft controllers. Controllers never worked on Mac.
Changes I made in March even broke Xbox controllers. I did a lot of UI updates and added things like the ship's Boost ability that were never properly mapped to a controller and I completely forgot to test controller support. In April I have built a new targeting and special ability system that further breaks controllers. It will take some thought and research to get them working across platforms.
So, I am pulling controller support out entirely for the April build. That being said, it's still a priority. I just need to take a step back and figure out how to get it working correctly.