A good number of AutoPot users don't have some kind of bubbler in their AutoPot or even reservoir and do rather well. Some add bottom perlite layers with AutoPots claiming or presuming this helps prevent saturation. I've used AutoPots filled with coco/perlite without mechanical aeration or bottom perlite layers and not had problems, got good results, etc.I think with auto pots its supplying highly oxygenated water where as a top hand watering only gets whatever is suspended in the water already and whatever it can pull in on the way down through the surface. Also with good watering practices as the soil drys out, in a good draining medium as perlite dries out it traps oxygen in its pores and overwatering pretty much voids that out.
Since you probably have some kind of bubbler in your autopot res you arent really "suffocating" the rootzone
My point is that a wet bottom, particularly if not allowed to dry out, and dry top is only a problem if there are any related problems, such as if the bottom is simply too saturated or the plant has not adapted to bottom feeding.