But doing it with a miner makes it so that you can do other stuff while it does its job and it is dirt you probably already have more then enough of it anyway. Another nice thing about the miner is probably the fact that after it is done you can let it search for ores.
Just as a warning I never used mekanism so I might be totally wrong about anything I just said.
You can, indeed, set several filters and mine ores as well as replace hardened clay with the same configuration. The main advantage to the Wand, however, is you can set the depth, so you won't run into more unwanted stuff if you just cut through one level of surface, and that the Digital MIner runs on its own. No matter if it takes time, you can do something more interesting than converting the surface of a dozen chunks with the Equal Trade focus.