Anywaaaayyyy....
I think this thread has potential, we just have to stick to the OP's question.
For the most part, I think it just depends on the design. I've had a few of these things apart. There are plenty of cheesy full/semi auto mechanisms out there. Usually these consist of thin pieces of stamped metal, nylon gears, and springs. In many designs, the tonearm has a rod extending down into the plinth that is permanently attached to a piece of sheet metal. The other components will usually disengage from this piece when the automation is not operating, but you would think that this would still introduce a measurable amount of resonance and mass to the tonearm. Plus, all of the other automation components might resonate, rattle, and "boing" inside the plinth, which could quite possibly introduce a measurable amount of resonance into both the tonearm and platter. Other designs, like Denon for instance, use a simpler, more compact servo/electromagnet system, which would appear to be more impervious to resonance. Sone of the linear trackers are also very good in this way.
No matter what, full manual is the simplest. Beyond the beaings, tonearm wiring, and possibly anti-skate or fluid damping, there is nothing else attached to the tonearm.
Regarding sound quality, there are other factors which are of more importance than the manual/semi-auto/full auto debate... Drive system, tonearm bearing design, thrust bearing design, platter mass, plinth mass, isolation, etc. A better quality, better designed turntable will always sound better.