I've been running into this same issue too. I want to use keyboard controls, but for some reason every time I start the game it defaults to Xbox controller controls. I currently have a Steam controller plugged in, but I'm using a M+K template to play the game with as Atom RPG's Steam controller mode has never worked for me.

After some testing, I did figure out a way around this: exit the game via Steam Overlay and your control method will be saved next time you start Atom RPG.

For some reason the game defaults to Xbox controls whenever you exit the game normally (backing out to the main menu and clicking the "Exit" button). But if you open up Steam Overlay (Shift+Tab by default) and click on "Exit Game", your control method should be saved!

One exception to this is if you play your game through Steam's Big Picture mode. If you play through Big Picture, the Xbox control method will always be the default, even if you shut down Atom RPG through Steam Overlay. I have no idea why this is.

Anyway, I've figured out a solution, but honestly I hope that this game gets patched at least one more time and this weird glitch is fixed.