Most current mods are likely to specifically work with the Steam executable, which is not really surprising since that's been the only (PC) version for over 3 years.
It won't be impossible to make the mods work with the GOG version, it will just take time and effort.
Someone asked the dev of Game Launcher of a possible GOG compatible version
Their response > "possible yes, not really sure how to check for legit versions tho, only way would be to check the hash value of the executable but i would need a gog.com version (and no, i dont want to buy the game a second time just for this)
thinking of it: because there is no DRM for the gog.com version you would no longer need a crack for a pirated version and thus a hash value check would not work so this is not an option"
edit: Link to that comment