I have the latest version of a gog game, but there's only an update for ms store version. Steam version, which is older than gog version, seems to work but I've only tried one option. Can I mess up my computer or game if I use a trainer that doesn't specify gog support, or lower version trainer on higher version game, which is my case? Every so often I come across an unpopular game that probably doesn't warrant an update, and there's been a newer version of the game come out.
I don't think you have anything to worry about. I've done that very thing a few times now. The Trainers just hack the code from the game. No danger to the computer. Some options may not work.