I can understand your confusion - the version on GOG and the version on Steam are different ports due to an accident at Larian that caused us to lose the source code of the GOG version. It's a pretty stupid thing, but sometimes things go wrong. So to make the Steam version, the port to adapt for Windows 7, had to be redone. Therefore, there's no relation between the GOG version and the Steam version, other than they're based on the same original game.
We're going to look at what issues might appear if we release the Steam version on GOG, and if none show up, we'll make it available there too, just to make future updates easier.
Sorry about the confusion.