Still. I'd expect them simply to provide that as a free digital update to those who own all the previous pieces. No reason not to.
Unless you're suggesting giving everyone the two expansion packs as a free gift, which is a little over-the-top in terms of "Unreasonable Demands", they need to maintain both sets of product codes - one for people who only own part of the set, and one for GOTY. So what exactly does "give everyone a free digital update" actually mean? They're already supplying the patch to everyone. They can't switch those who own everything onto the GOTY product code, that would mean that (for example), Gog users would then own two copies, and console users would be screwed on their savegames.
I'm really not clear why "They're exactly the same" isn't stopping people asking for this. The only difference is during a download, and that's trivial. For everything except manual download from Gog, you already get the latest version. The most they need to do is update the Gog manual download to take you straight to the current version, instead of (earlier version + patches), and they'll probably be doing that anyway, they have done twice already.