Greywolf1: I don't know what exactly your issue is (you don't provide enough information), but "incompatible" means incompatible, not "can't manipulate". Your "DF GOG Cut" is based on an outdated version of Daggerfall Unity (DFU), and many mods contained in the GOG Cut have been updated to the most recent version of DFU, and at least some of them are now incompatible with the outdated GOG Cut version of DFU.
The GOG Cut is a package which hasn't been updated for a long time. Will GOG update it in the future? I don't know, but I doubt it. If you want to continue playing the GOG Cut, you're probably stuck with the version available from GOG. It's the risk of using packages like the GOG Cut.
PS: In theory, you could try to update DFU to the latest version manually, and then to update the mods manually. It may work, but there is no guarantee that mods not updated to the latest version of DFU continue to work, and that your savegames are compatible with the manually updated package.
Thank you for the reply. It agrees with what I was afraid of. It isn't a bad game as the GOG cut but definitely outdated as far as the modding scene.