Strange but just noticed that the dotemu version is no longer on the list of versions you can rollback to (Version gog-1). Either it got deleted or pushed out by recent versions. So I guess you can't achieve those old cheevos anymore, unless you have an old manual backup or something.
You can. Just go to settings, turn on Beta Channels, under Channel select "Add Private Channel" and enter the password "dotemuversion" then select "DotEmu 2017 Version" from the Channel list.
I know it is not exactly 0.0%, but every achievement for the fighters is on 0.0% feel at least suspicious.
I defeated Kain and got the end credits rolling.
There is an in-game section called achievements in the Code Mystic version (if I am not mistaken), there I unlocked a picture of Terry.
The in-game achievement UI is getting its unlocks from the GOG server, so if you see it in there, then GOG says the achievement is unlocked. It does take a few seconds for it to turn up in the client. Are you still not seeing it unlocked today but are seeing it unlocked in the in-game UI? If that's the case, it seems more like a GOG issue.
(We're Code Mystics, BTW.)