I have not head of anyone layering the beds with different material, but I would assume that it could be done. Might make clean up between use a little more labor intensive as you would have sort out the materials for cleaning. Not sure about the "mat/foam" as the roots would clog the foam.

I have been looking at different siphon systems as well and kind of like the idea of the external drain systems like an external loop siphon does seem simple and you idea of the filter should work well as long as there is a gap before the drain. I am thinking it comes down to preference and what works for you. Give one a try and let us know what you find. i will do the same.

Jason