JudasIscariot: You can see your game version in the game :) Just open the menu by using the big power button in the upper left corner of the game and there's your version number :)
MadnerKami: Um, yeah. It's even listed in the download with the according info, which lead me to the solution in the end. Problem is just, that I simply do not expect a patch to exclusively work with the base version of a game, when a different patch just came out about two weeks earlier. Given the bugged state of the vanilla game, I'd expect a new patch to be able to work with the previous patch instead of necessitating the vanilla version that nobody in his right mind would play.
I have to agree with this.
While the end result wasn't a MASSIVE hassle for me (reinstalling the vanilla, then applying the latest patch), the only reason this patch fails is because the GOG patching team actually went overboard with the checks it does.
Once the game directory has been chosen, all the patch should do is copy the new files. If there are already files with the same filename, then it should just overwrite.
Unfortunately for each file to replace, it checks the original, and if this doesn't match up to the original, then it won't copy the new file!! Which is way too much hand-holding safety crap - if I've told the installer my SRHK is in that directory, then I expect it to overwrite everything as if that's the case. If I've stuffed up then too bad - that's my fault - but the damn installer shouldn't decide not to copy a new file because the old file doesn't match the exact version it's thinking of!
TL;DR: Adding this extra safety "feature" to the patch file is unnecessary, serves only to annoy as opposed to protect, and no doubt took time to implement. So GOG took longer to make a patch more annoying in other words.
Suggestion: In future, don't bother with all of that "safety" crap. Just get the patch to copy the new files into the given location and be done with it - that should be simple and fast to do, it ensures better patch compatibility, and could mean the patch gets released sooner.