Rather than making a really long subject, I thought that would be enough.
I am making cars with most of the upgrades listed in the car design window, however they show a negative premium, and price even though they appear on the finished car.
Gry.
Hi, you have clearly set those features to appear on the car in the design screen, but have you purchased and installed the appropriate upgrades on each slot? You need to do that too, and at the moment, the game does suck at explaining this 
Yes, they are purchsed on the slots, Otherwise I think you get the dark red with the ‘-’ like the top two, as they are not purchased on the slots.
I don’t know if this is something to do with resuming from a saved game. I’ll see what comes up on the next play through, it might glean more information.
Gry.
Aha sorry, I didn’t understand. Yup this is the current financial model, which at the moment is penalizing those features because they are in ‘every’ car, and thus you get a lower price for them. That changes in the next build, as I agree its pretty confusing.