The listing of the Base Game, Underlord Edition and Ultimate Edition are to ensure parity with the Steam Store. If you note that the Steam Store does, in fact, have all three of these versions as Bundles. See the attached image to see how this looks.
As GOG does not have support for this form of in-line listing of Bundles on its store page we had to list them as separate products. Totally agree that it's not as intuitive or friendly and can lead to confusion for loyal GOG Customers.
The other option was to not offer the bundled editions and their associated discounts on the GOG Storefront. This wouldn't sit well with us as it would needlessly punish GOG users for their choice in store. Instead we opted to do whatever we can to ensure that whatever deals are offered on the Steam Side are present on GOG and vice versa, so no one feels they're getting a bum deal.
Hopefully in the future, as GOG continues to expand, improve and evolve we'll see additional options for publishers to offer deals in a more clear manner and we can do away with needlessly confusing SKUs.
It's unfortunate that in this case you were charged more than you may have needed to be. I wish I could do something to help you out on this because we certainly don't want players to be overcharged. My advice would be to reach out to GOG support and see if they can help you.