You could have the same issue with a root tab filled tank. I'm general its not good to uproot established root feeders. And definitely need a cap over soil, although the clay addition to mts helps serve as a flocculant.
I don't do the potting soil method, but i know with MTS that if you were to start turning over the soil for some reason it would make for a cloudy tank. It eventually settles, but I could see the potential for an algae bloom if that happened, although I've not seen it in the tanks that I've had to uproot and rearrange.
DIY root tabs, either osmocote or if you are feeling adventurous, mixing your own, work quite well and are much simpler than a substrate change. One downside to root tabs is if you uproot something, you may get a large red spot on the substrate or a red cloud in the tank. Or if you are using osmocote you'll end up with little yellowish spheres everywhere.