You made some good points. It will require more energy to "spin up" the
non drive wheels than the drive wheels due to inefficiencies. As you
said, the flexing of the body won't be significant unless your driving a
Mustang without subframe connectors.
Additional inefficiencies will come from the deformation of the tires.
For the sake of this discussion lets consider the drive axle the source
of the energy, and all 4 tires/wheels are the same weight and size.
Consider only the portion of energy needed spin the tires/wheels from 0
to 60 mph, the simple analysis says energy to "spin up" 4 tires/wheels
will be 4 times the energy to spin up one tire/wheel. I'm sure someone
can look up an equation for stored energy in a flywheel (tire/wheel).
The drive wheels are driven directly from the axle so there won't be any
inefficiencies for the drive wheels. The other wheels will get their
energy from the drive wheels, thru the inefficiencies of the drive
tires, and thru the inefficiencies of the non drive tires. The
associated rolling resistances will manifest itself as heat (lost
energy) in the tires.
I would now conclude that the lighter wheels should be put on the non
drive end if all you're interested in is acceleration.