Ok. so this is why i would never grow plants in a container in a tank.
1. it limits root growth.
2. the water flow is either non existent or marginal
3. if you 'seal' the top with stones that will just compound the problem unless you sort of dig through the sand once in a while.
4. I've seen it done a couple of times - with many types of substrate, and boy did those roots rot! the smell was enough to kill me hahaha.
its different in a tank where you have lots of water flow, the occasional gravel vac and plants being shifted around sometimes.
one way to over come this, or reduce the side effects is by using a normal ceramic pot with the hole at the bottom. just put a small convex piece of pot or something over the hole so the substrate does not come out. you'll find the roots come gushing out.
you could try some stem plants but your mettnys will eat them.