GOG version of 1.7 have working gamepad support - all xinput, all directinput, on linux: xpad and even on MacOS.
Sadly not. Gamepad input simply does not register at all, no matter what I do. All other games that have gamepad support on macOS work correctly, so it's not an issue with my computer. Especially considering that Hyper Light Drifter, also made with GameMaker Studio, does have working gamepad support. My guess is that it's something to do with the version they're using. So whatever it is, use that one, and it will magically fix everything. ;) (Yes, I'm aware it's not that simple.)
I don't really care about version numbers or anything. I just think having different numbers on GOG and Steam has created some confusion. If I had known 1.7 on GOG is basically 1.9, I wouldn't have started this topic. I mean, there's still a problem, but it's apparently not what I thought.