Cindy - I have them in my Dirted tanks and in my submersed bare bottom grow-out tank that I grow plants in Clay pots in. Never have I see MTS dig up dirt. In my tanks the Cap is 1 to 1.5" deep. In the clay pots maybe 1/2" deep.
About the only observation on this I would offer in my tank with Sakerete all purpose sand with has fine sand to very small pebbles. I feel it separated faster with the snails.
I cull about every two months. Algae wafter in a net over night. I pull everyone out sm. & tiny ones go back in to work...adults got out.
The benefits of a healthy snail population (MTS & Ramshorns) far out weights any perceived negatives. I would not own a Planted tank without them.