Puzzling Pioneer volume differences

I've got a vehicle here with Alpine 6x9's in the doors hooked up to a $200.00 Pioneer HU using the HU's internal 50x4 amp.  It plays at a comfortable volume with the HU volume at 15-18. The other vehicle has a Pioneer DEH-780 feeding into an Alpine PDX 4.150 then into dash firing 5-1/4" comps. With gains properly set; the second vehicle has to be cranked up to 45-50 on the volume scale for comfortable listening. All loudness or boosting functions are switched off on both units.

Why the difference in volume especially with vehicle number one using the internal amp? Is it because the speakers in vehicle one have a larger cone area?