Sorry for the delay, I was away on vacation.
So firstly, yes, the GOG version is compatible, in fact it's that version that I made the mod specifically for. You do need to turn off the 'Cloud Saves' as mentioned in the installation instructions though.
If you are looking to play the upgraded version of the game in 256 colour, then the good news is that 'Ultimore: A World Divided' is included in Pix's Ultima Patcher so you could do the whole thing in one hit and it might be a little easier to install too.
https://www.pixsoriginadventures.co.uk/category/ultima-patcher/