Shouldn't be that difficult to down- or upgrade to the required version (via a patch or mod), If it's just slightly different?

There is no way to do that. Some smaller mods are already incompatible because the modders just don't bother to make a GOG Skyrim compatible version.

The only hope in this case is that GOG will update Skyrim accordingly to work with Skyblivion. But I don't know how likely that is.

That's cute! While you kids play around in a toy version of Nirn that had all the edges smoothed off (and missing several schools of magic), here's a project to put all of Tamriel into Morrowind that doesn't care what version of the game you have*.

*I doubt it'd work on the Xbox version, though.

Well, this one will wait for Skywind. I do own Morrowind here on GOG, have it ready to play and everything, but it didn't quite grab me yet. Maybe I'll give it another go waiting for Skyblivion?

Also, update: maybe a false alarm on not supporting GOG? I'm now being told they want to try have the GOG version supported. Still, doesn't change my original point - the version difference between GOG and Steam versions is causing issues for modders and people who want to use mods.

You and what army? I killed their dunce of a leader and didn't even assume the role!