I hope I am just missing some detail, but the season pass with 3 dlc is actually more expensive to buy than each dlc separately. That goes against common business logic. A season pass is a package deal and should naturally come with a discount to entice the customer to buy more than just one or two.

And this is not the first time I stumble upon this either. Is this GOG or the publisher messing up? Does anyone know?

I don't know it does seem a little off.

But my suggestion is to strongly consider if you even want "Beneath The Stolen Lands". Because if you really wanted a rogue-like dungeon mode you might be better off getting "The Treasure of the Midnight Isles" DLC for Pathfinder: Wrath of the Righteous.

I don't personally enjoy DLC that does not add to the main campaign though so I can't really recommend either of those DLCs.