What I am saying is that the excess in the bottom, after watering doesn't need to be emptied. It will wick back up into the medium as it dries out, thus compensating the limited depth and water retention capacity of your bed. The transport mechanics of your set up won't let it sit and get stale. The lowers will tend to hang in the juice, you can try tucking them while you feed. Those will be the first to get consumed by the plants and fall off anyhow so don't get too attached. lol forgive the pun
It's interesting how your treating it more like a flood and drain minus the drain. The first set up like this I made I actually used air and diffusers in the pearlite and kept it going like a lower res. Kind of a hybrid semi. I have recently seen a company making the same set up in a pre-packed unit too.
Meh, it's apples and oranges. Your doing great and I certainly see no harm in your process!