Interesting. This would be a perfect Science Fair type of experiment if you grow the same thing on each side. I agree that it is easier to start seed in soil, so that makes sense. When I had mine, I'd start from seed in a little dirt cup. I believe I got a piece of pvc and pushed it down into the clay pellets to make a hole, tried to gently knock all the dirt off the roots, slid the whole plant into the pvc pipe in the pellets, then gently pulled the pipe out and held the plant in place. It worked well enough, but I'm sure there is a better way.

Is the drain pipe above the barrier between the rock and soil? How does the water get into the drain pipe? Couldn't you just drill holes in the base of the tray under the rocks? I assume the barrier between the rocks and soil serves the dual purpose of keeping the soil in place, and being just permeable enough to allow the water to slowly drip through, like a coffee filter?

My biggest problem was that I didn't have adequate lighting. What is your light set-up? I'll go look to see if you have a video about the lights right now so no answer necessary if you already covered that.