Better to tighten with it jacked, gravity actually makes for more effort simply lifting it back in place, technically that affects the torque slightly. Really no difference though. It will be easier to move plate around with it jacked of course. I never torque to spec there anyway, simply get it tight works all day long.
A natural law-harder rubber just like poly vibrates more. No, it will not affect CV joints at all, rather your comfort...........