Similarly, one wouldn't stack 2 filters on their house furnace either. It's hard on the blower motor. Who wants to replace a blower motor? It wasn't fun in my Saab hanging upside down in the passenger footwell. Probably isn't fun in the GTI either.
I am not a filter or blower expert but you have me thinking.
A clean filter should be able to pass more air than the blower can move.
In a well designed system the filter surface would be large enough to still pass enough air thru even if 50-70% full, maybe even a higher percentage clogged as this will protect the blower motor.
So with two new filters the drag on the blower should not be much.
If we run the system for 6 months, the car with 1 filter should pass as much air as the car with 2 filters. They both have filtered the same amount of air. The 1 main filter will be dirtier than the main filter on the 2 filter car. So at 6 months one car changes the $20 main filter while the other replaces the $4 filter. Maybe every other filter change now one would change the main filter in a dual filter car.
Also for thought.
Most cars use a squirrel cage blower. If you block off the intake, this blower should continue to spin with no extra load. A squirrel cage blower works well to flow air as needed in a car but is terrible at blowing with force or creating a vacuum. Again not an expert in detail but from hands on experience I think the blower will be ok. In fact with cleaner the air in the system it might last longer. It also might blow more air over time as squirrel cage fins can collect a lot of dirt and this will reduce efficiency.