Right, it is much easier for them to schedule production, parts, and other things if they know that the next batch of cars they build all have larger batteries, which also means dual motors, and the SC enabled. As opposed to 300 with larger batteries, then 500 with dual motors, then 200 with both, then some with batteries and SC but not dual then dual motors and SC but not ...In my mind this is simplification. Sure they are base options, but once you "level up" to a larger battery, it's assumed you want the other two options, so they're no longer options, they're just included.
That's a big factor in why you get a package discount over the ala cart pricing.