I can explain this :)
in older GOG releases, the version numbers that were in use were the installer version numbers, not version numbers that were relevant to the games themselves. This practice was apparently phased out during 2017, with the intended purpose of allowing developers to include the actual game version number instead, as it's obviously more informative than the installer's version number.
And specifically for this game -
The installer with version 2.5.0.12 was released in 2016, so this version number has nothing to do with the game itself - it's the GOG installer version number.
After that version was released, and before the next one, GOG changed the versioning system as I explained above, so for the next version, the actual game version number was used, which is 2.4.800398 (you can see it in-game at the bottom-right corner of the Options menu); so it's actually not a lower version than 2.5.0.12, because these two version numbers are not related to each other.
Bottom line - "2.4.800398_(12443)" is the latest version.
Note that there's another version-related issue with this game - the devs didn't update the in-game version number in the last three versions, so if you enter the Options menu in all three versions, you'll see the same version number - "2.4.800398". This is a very annoying and common bad practice which I simply can't understand - why is it so hard to bump the in-game version number for every new version? It's just devs being devs I suppose :D
Anyway, this issue isn't completely relevant to the confusion that's discussed here, but I thought it's a good opportunity to rant about it lol
