Hello, I've been playing for a few days on my brother's steam account, and now that I'm back home I'd like to buy my own copy. I'd rather get the GoG version, but it would be great to know that I'll be able to move my save over. Can I expect this to work, or could there be some kind of compatability issue?

The game itself is completely DRM-free, so there's no reason why the Steam version saves should be any different. I can't confirm it because I don't have a Steam version, but I would put money on the saves being completely compatible, unless Steam adds something, which would be a completely shitty thing to do.