Notice that this is a penalty that never existed before tucked away in the description of the piece of equipment that removes it. That's called terrible formatting and design.
Most people just ignore the fact that the modification exists at all, and treat it as more a question of good sense.
Not true.
It is a rule that is in the core rulebook. Page 420, gear chapter. "Using Unadapted Gear"
It is however, a rule that is based on the increased Lifestyle costs for living as a Dwarf/Troll. One could assume that a Dwarf/Troll that has been appropriately paying their lifestyle costs get all gear properly adapted to them as part of their increased Lifestyle costs. The modification in Rigger 5.0 is for adding that modification to a vehicle post-production. Meaning that if that dwarf gets a car with a five-finger discount, off an enemy that no longer has need of it, etc. they need to modifiy the car to have it properly fitted to them.
Likewise, I've made riggers that have added the Metahuman adjustment to a vehicle to represent that some of the seating in a passenger vehicle is adapted to allow for Troll passengers (for example).
Also, to answer the original question. My ruling would be No, you do not suffer the gear size difference penalties while rigging/controlling a vehicle without manual controls. In those circumstances there are no controls to impose the penalty. At best, you could claim that the seats might be uncomfortable for a dwarf to sit in if they are "unadapted," but nothing more.