You're confusing dealer-added options with factory option packages. Cars bundle features together because they get better economies of scale by making only a few different versions of a model ("trim levels"), instead of letting everyone mix-and-match parts. Factories don't work that well when all the units aren't the same.

Dealer-added options aren't added at a factory, they're added at the dealership, solely for the reason of inflating profit and convincing customers to roll the cost into their loan.