The issue involving Controllers not always working has now been fixed. Occasionally when starting up the game it would not recognize the controller, but it would if you turned it on after you launched the game. The game originally had Steam Input opted into for the various controllers. This has been turned off and fixed the issue. If you are still having issues, please make sure that Steam Input is not turned on.
If you have any suggestions, bugs or issues - feel free to reach out via the Steam Forums or on Discord.