FWIW, I ran only an AWR front motor mount for awhile (also a SU front mount alone). I've since swapped front mounts 3 or 4 times, and rear mounts twice... in each case, the bolt going through the mount came in and out fairly smoothly, so I don't believe the aftermarket mounts inherently cause a different geometry. What is possible is that running only a front MM can change the axis on which the motor pivots during acceleration/engine braking. I suppose it could also depends on the condition of your other mounts.
As long as we're on the threadjack, yudkib, is this groaning a single short sound (like a suspension groan), or is it a continuous noise (say as you're accelerating through 2nd at WOT)? If it's a continuous sound, I'd be strongly leaning towards a blown motor mount transmitting vibration when certain torques are acting on the engine. That rear mount REALLY transmits vibration into the cabin well, since it's basically bolted to the firewall.