While it's true that GOG and Xbox accounts are separate (naturally), there is a precedent for cross-play functionality even between separate platforms. Street Fighter 5 enables cross-play between PSN and Steam users, and Rocket League offers Xbox-Steam and PSN-Steam cross-play. And of course, a number of GOG titles offer GOG-Steam cross-play, which is basically exactly the same principle as console-PC cross-play.
Incidentally, the Gwent page has this:
Do you support cross-play / cross-buy, i.e. purchasing items on platform A and using them on platform B / playing with gamers on other platforms?
CROSS-PLAY: We can confirm cross-play between Xbox One & PC, and PlayStation 4 & PC. Xbox One and PlayStation 4 cross-play is not possible. Please note, however, that Friend Matches are only possible within a given platform, meaning that you can only challenge a friend to a Friend Match if they are playing GWENT on the same platform as you are.
CROSS-BUY: When GWENT launches on Windows 10 as an UWP (Universal Windows Platform) application, the account between UWP and Xbox One will be shared. That means progress and cards are shared between both platforms. Otherwise, every platform is independent and your progress will not be synchronized if you switch platforms.