That is not true. A lot of the stuff on GOG has native Linux versions and they work hard to make them work as best they can. Just because their own games don’t have a native port doesn’t mean they don’t care
Witcher 3 also had absolutely no reason to have a native version (other then make the reeeeeeeeeeeeeeers shut up) and realistically requires more work then it is worth (yes I know MUH LINUXers can’t understand that argument, but that doesn’t make it any less true). Witcher 3 ran basically perfectly on WINE from day 1 so why waste developer resources on a platform that in the long run results in more work then it’s worth? And we’ve seen how the Linux community can be absolute dickheads with Witcher 2. If it’s not absolutely perfect on every single distro “those people” will ruin it for everyone.
And also remember Witcher 3 released at a time where Linux gaming was still absolutely atrocious, it certainly is not as it is today (and even now it’s far from “click install and go”).
Back to topic:
I have not tried it myself, but have you tried just installing GOG in WINE and using the sync that way? You can (probably?) symlink the save files into whereever GOG needs them to sync and let it do it that way.