One of the benefits of a deeper rear wheel is that you can (safely) run a deeper front wheel. Having a deeper front wheel (which as you noted as a better impact on aerodynamics) than rear can be problematic in crosswinds.
The logic if I recall is if the center of pressure of the bike profile is too far to the front of the bike (in front of the center of gravity, I think, but it’s been awhile since I’ve read this) then crosswinds will turn the front wheel instead of just displacing the whole bike sideways.