Seems like its a fixed price. Besides the "completion" where you don't pay stuff you own already in a bundle, the base discount of the bundle is added on top the individual prices. The fixed package price seem not to care anything going on, even if it ends up being more expensive. At the very least they could cap it at to the sum of individual prices.
Usually if I buy a game on its own, and Steam notices there is a bundle where you could get the game cheaper, then there will be a note on the cart page before checkout. But there is no notice for this case (on Skyrim+Anniversary) with packages. So I thought it might be a bug.