It depends. No mods are really guaranteed to be 100% compatible and obviously Masterwork is a big mod that changes a lot of things. On the other hand it keeps a lot of vanilla DF is intact so it's surely at least "close to compatible" with a lot of vanilla mods.
If you created creatures or plants and tossed it in it would most likely be fine. Unless, for example, it has the same name and duplicates something preexisting.
If you start doing reaction or entity modding then you should learn how Meph's standardized materials, & maybe changes to professions, work first, and be prepared to keep learning and debugging as you go along. If you wanted to merge Masterwork with, say, Fallout:Equestria obviously you can't just paste them together, you would probably have a couple full weekends worth of work on your hands.
