After reading above and with such suggerstion:
I’m follower of this solution. So ground vehicle should have dedicated slot under air vehicle and should not limit dropship’s capacity for soldiers. But in such case I would lower aircraft speed by some factor (maybe 25%) and definitely would change one other thing related to aircrafts (but that won’t be part of main game I suppose, so will only be applied in my balancing mod - if I will get to it after releasing official mod support).
EDIT: 25% slower speed means also 25% lower range before refueling (so their area of operation will be only 56% of original one). Thus dropships with ground vehicles would be slower main forces, while dropships without them would be faster responce teams.
And beside above mentioned modifier in my mod, there will be also another one quite significant making changes to capturing aliens.