It's been ages since we've purchased a new car, but can't you just check the box for "$FOOBAR" after checking the box for Package A? Our Leaf was pretty much pre-built with few choices outside of packages, but we did that with our Scion. Additionally, though my BMW motorcycle came with a "package", I could still get stuff a la carte. I'd just have to wait for BMW to build it and ship it, instead of riding it home that day. (Or in my case, the dealer has the a la carte items on the shelf. They sent me home with the taller windshield in a box, for example, and I bolted it on myself.)
OTOH, I'm using a motorcycle, an early-adopter electric car, and a quirky little off-brand Toyota as examples. Probably not the best examples for sussing the average car buying experience.
As a result, I don't buy package B, or even don't buy the car at all and go to another comparable model.
I had no opportunity to explain why I didn't buy package B to the manufacturer, so do they even realize they're missing out because of that? I'm sure I'm not the only one.