My friend had told me that Divinity series is a good thing to play with a girlfriend in co-op, so I bought Divinity: Original Sin 2 -- Eternal edition. It looked like it contains everything from everything, all the manuals, soundtracks, etc. So I just bought it for myself and for my girlfriend too.

It turned out, however, that:

1) GOG has a lot of things that can be found if searching for "Divinity" in the store. 13 items, to be exact. Many of them overlap.
2) Among all the games in the series, only Original Sin and Original Sin 2 have co-op. OK, my fault that I didn't check it.
3) Dragon Commander is not part of the pack. I bought it anyway, most likely by mistake. I don't really regret it, because it was on sale and hence dirt cheap, but it is not listed to have a co-op.
4) Eternal Edition, which is the most expensive pack (which usually contain everything from everything) is not a pack that contains everything, not "the" pack.
Original Sin 2 comes in Standard edition, not Collector's.
5) There is not even an upgrade option available. Hence, now need to buy Collector's edition if I really want all of the additional stuff.
6) This additional stuff includes manuals and the official strategy guide. I mean... really? It's not included in any other pack?
7) Sir Lora seems to be a nice DLC that is very cheap, but... is simply not listed under "buy series", and also not included in the Eternal Edition.
8) The sale is now over, so I'll need to pay the full price now if I decide to buy Collector's edition.

Honestly, I am very frustrated.
Just... why? Why does it have to be such a mess?

That sounds more like a dev/publisher issue. GOG doesn't really get to dictate how games are packaged or sold. If you want the dev/pub to organize everything into a megagrandpackage now that the dust has settled, that would be the point to contact.

However, I will note: On the game card of Divinity 2, there is a dropdown menu where you can select your edition.

Though perhaps, you could tell GOG to bundle the Director's Cut of Divinity 2 as a whatever within the Divinity 2 game card.

For 4) and 5), I just checked the download page for each game of eternal edition. It seems like the other stuff, which is in the collector's edition, is contained in the download page of Beyond Divinity and Divine Divinity.
Please check it out to make sure if it is the exact file which should be contained in the collector's pack.
I just noticed that, but haven't checked yet for sure.