The Steam version is what went into the anthology (possibly with additional bug fixes; I haven't installed it yet), which is what the GOG version was updated to. While I have not tested it, I'd say the batch file modified for the Steam version should work fine with the new GOG version.
The problem with the disk version of the batch file was that in the download version of the game Larian changed the folder structure for the game. The disk version had most of the game files and folders in the '..\Divine Divinity\run\' folder; the download version got rid of the 'run' folder and moved its contents up. That isn't the case with the different download releases.