You pretty much said it. The Steam version often has all sorts of stuff for Steam integration... and the Steam version is the default version. So various hooks for achievements and networking and mod installation may be different. Messing with any of that could easily break something. Furthermore, GOG does have its own API that some games use (again, for achievements and cloud saves); so if a game has chosen to use those features they may accidentally break something.

But even aside from possible difference between versions; bugs in the game itself still have to be addressed on every platform. Even if they don't bother testing the new version, they still have to at least push the update - which is still more work than zero work. This is why it is fairly common to see games that are under active development only have their beta version on Steam (or in some cases only Epic), even when they intend to launch on a bunch of platforms.

So for some games (certainly not all, but definitely some), patches come on Steam first and GOG at some point later. Maybe a day later, or a week later, or in some rare cases not at all. Similarly for DLC. And that definitely isn't GOG's fault. There isn't really anything GOG can do about it. It's just a side-effect of Steam being the far bigger platform.