Those are GOG installer versions, as in, the files you actually download from GOG. It is not necessarily related to the game itself.
That's where the confusion lies. Sometimes it's because they are using a newer installer program, sometimes it's because the original game got updated to a 2.x version and sometimes it's because the game is now HD.
Or at least that's what it looks like to me.
Personally, I wish they'd adopt a more consistent approach to versioning. Especially since they're using some many decimal points anyways.
My guess is that the Linux games are going to have that 1.x designation for quite some time, unless GOG creates a specialized installer program rather than just using debs or folders.
I never pay attention to the installer version. If the game is updated, I check the changelog. Most of the time there are fixes for the games, but many times it is just administrative stuff or additional work on the installer itself, nothing that anyone with a functioning game needs.
For actively patched games however I think it needs to be more clear what GAME VERSION is included in the latest installer or installer patch. I think we are in agreement there. Still, GOG puts out changelogs almost immediately for every installer update, so if you're interested just check the game forum. It takes minimal effort for the customer to inform himself.