The Witcher 3 GOTY is treated as a separate "game" altogether. I have both the above and the GOTY (kindly added by GOG automagically), since the GOTY was not around when I bought The Witcher 3 on GOG (just the base game + DLCs).

P.S.: The GOTY already includes the base game and all the DLCs, so there's really no reason to buy them as well. The GOTY is meant to supersede the "standard edition" and offer an all-in-one package.

This is just an idiosyncracy in the store itself. I have the same thing happen here basically. The Witcher 3 GOTY is nothing more than The Witcher 3 plus the 2 expansion packs plus the 16 free DLC all bundles together in one single installer patched to the latest version. It contains zero extra content, features or differences at all other than just a convenient repackaging of the entire game. There is no reason to buy the non-GOTY game and no benefit of it whatsoever.

The store is also a bit hit-or-miss in identifying when you already have parts of a bundle.

For example, I am continually offered "Neverwinter Nights Enhanced Edition Digital Deluxe Edition" for full price (around $68), even though I already own every item in that bundle except for one $3 soundtrack. Just for kicks, I tried ordering it and going all the way up to payment confirmation to see if I'd get some kind of discount. I didn't complete the order, but it sure seemed like it was going to happily charge me $68 for a bundle that would have only added a $3 soundtrack to my library.

However, I've also seen some bundles that have correctly identified that I already had the base game and offered me the expansions/DLCs at a reduced price. I was pleasantly surprised to get a discount on a Battletech bundle because I already had the base game.

So, if you already have some content from a collection - it's worth looking at the bundle cost vs. buying the remaining content you don't have individually. And definitely don't hesitate to ask the community: "I already have THIS... will buying THAT give me anything more?"