If the difference in tire height is 3% on an axle, yes, it can cause AWD problems. 3% is the tolerance limit for variance.
As it sits, the tread depth difference is not significant to AWD except if it causes traction differences. Traction differences will cause the ABS to modulate wheel speed accordingly.
Symptoms point to PTU though, especially if they occur under light throttle at cruising speeds. I believe there is a TSB on that somewhere.
RPM flutter is a completely different animal and could point to torque converter.