I went back and checked and it seems I kind of remembered it right, when it was first released on GOG there was some kind of version incompatibility with the Steam one: Link
You can see it in the SKSE page too, there’s a version specific for GOG: Link
But reading in the gog forums it seems this is not a problem for Fallout 4: Link
Modding will work just fine. It’s the same game of the year edition that was released years ago on steam.
The Skyrim special edition that you’re thinking about took the native 32 bit Skyrim and translated it to 64 bit. This broke most mods.
I went back and checked and it seems I kind of remembered it right, when it was first released on GOG there was some kind of version incompatibility with the Steam one: Link
You can see it in the SKSE page too, there’s a version specific for GOG: Link
But reading in the gog forums it seems this is not a problem for Fallout 4: Link
We’ll have to try and see! ✌️