Can replacing the transmission axle and NOT realigning the front end correctly cause the rotors to warp?
No, it would just cause the car to handle poorly and wear
tires.
Rotor warping is caused by heat. If the vehicle carries heavy
loads and routinely builds a lot of heat stopping it can cause the
rotors to warp.
Also, if a caliper does not completely release the rotors can
warp.
Sometimes they just warp with normal use.