In a sense, you are correct, in my Witcher 3, if I wanted to install manually, I have the setup for The Witcher 3, the setup for the Witcher 3 Free DLC, the setup for Hearts of Stone and the setup for Blood and Wine. All quite nice, and I'm happy.
Now if I'd bought the GOTY, I'd have 1 setup, setup_witcher3_en_goty_2.0.0.51.exe (according to someone that bought it), and I'd be done.
Obviously, I'll install through Galaxy for convenience, but it's a matter of principle, you know? I mean, if they are identical, what's the harm in unlocking it? For example, I bought the Season Pass that included both the major DLC packs. And when those were released, they were indicated as Owned in the store page, even though I didn't buy those exact ones. So, if the GOTY is identical to what I already have, just put it on owned.
I know, call me OCD, but I can't stand seeing that one unpurchased listing in the "People who bought it also bought" section. It makes me want to buy it just to get rid of it, and that would make me very upset with GOG. :)