During Deadfire early build testing GOG patch downloads were noticeable bigger as well. Devs explained that gog doesn’t allow to patch files - so if there is a small change in a file, rather then downloading and patching the change, gog requires a download of the entire replacement.
So gog is just less advanced in that regard. It is also could be possible that download could be made smaller but Larian doesn’t feel it’s worth optimising patches for different clients (and what I expect to be relatively small portion of player base on GOG) and makes GOG users download the whole thing every time. Or maybe it’s GOGs doing, I am honestly not sure how it works.