Thanks for your detailed reply!
About hydroton under pots: Okay. The 1L airpots have a small air gap under them, but I have usually
added a wick to give the roots a head start until they grow past the air gap and down to the tray. With the solo cups, I don't start bottom-feeding until the roots have spread to the hydroton layer, which is probably small enough that the autopot's fill layer should still contact the coco. I've added that because I noticed that the roots in airpots really liked that small air gap, and all my solo cup plants responded very well to adding a ~1/2" layer of hydroton. Before that I had roots plugging all the holes I've drilled in the cups and causing drainage problems, then root rot.
Putting something inert between the pots to take up volume in the tray is an
excellent idea, and would allow some control over how much it floods, which could be fine-tuned over the grow.
Stirring the reservoir: I previously used an airstone in my reservoir, continually bubbling and buzzing. (The venturi aerator should be much quieter.) A little aeration on a timer would probably be plenty. I haven't had problems with nutrients coming out of solution, but I will have a filter on the autopot intake just in case.
I will check out the Troubleshooting the Autovalve thread, and if I decide to go this route for my next batch (likely around late December/January) I'll tag you.