So all you need to do is allow water to build up and stay in the bottom so you don’t get those ugly roots.But having a pump to drain them is weird. So you’d have to change it to top feed so gravity returns it to the res. Everything at same level.
Years ago I had a similar system. Clay pebbles in pots. I had the same problem so I raised them up and aerated the water below for the roots to live in.
Here’s a pic. You can see the net pot holding the pot up off the bottom. I just put a short pipe in the drain to raise the level. Then I added an air stone.