You can reverse the trick too – you should be able to simply drop any mod into the mods folder within the Steam version of the game, and it should just run straight out of the box.
Buying the game through Humble will give you a Steam key, so you should be able to dig that out and unlock an “official” in-Steam copy. There’s no difference really, except that it will unlock trading cards and the overlay will be officially supported (it normally works with non-Steam games, but it won’t automatically bring up e.g. the Stonehearth community hub within the overlay.) With an official copy you’ll also have easier access to Workshop mods – you’ll be able to simply subscribe to them and Steam will magically make things work. It sounds like a major difference when put like that, although given that it’s not hard to do manually when you know how it’s only really a big deal for people not familiar with modding heheh.