this is an issue (or i would say a sabotage) brought by the devs on the 1.6 gog build (before leaving)
the saving of progression, unlocks or other things was clearly tied to the steamAPI and steam userprofile (which cannot be found on gog build/installation) to prepare for the future of mobile-businessmodel microtransactions the game migrated to...
version 1.5 (or at least version prior to 1.6) would work fine and save unlocks and progression; sadly this version is not downloadable anymore as offline installer
only "issue" of the 1.5ish version is that it was installing redundant full asset files for both x32 and x64 versions (while all the files are strictly content-identical and size identical), but you just can remove the version you dont use - 32 or 64 bit - to halve the install folder size .
now, though, we would need GOG to put back the 1.5 offline installer in the customers library for downloading (bug fixing between 1.5 and 1.6 ar eminors, most of the changes were made to prepare the migration to steam and microtransaction stuff)
i dont know if the game would have a rollback feature on galaxy (but not everyone here want to use galaxy anyway, so)... afaic, i kept all my gog versions of the game, and incremental patches when available... would i have not done that, i would be stuck, like you, with a game version that was broken (and probably broken on purpose)
League of Geek were backstabbing gog customers hard... but gog could at least leave us access to previously working versions ?