The sand disturbance could be mitigated by raising the water level in the fuge area, the micro bubbles could be lessened if the water level in the pump return area was raised.

I dont understand the frag shelf flow. How about one long sand bed and just put a portable shelf in the center section. The sump sides would have to be taller for overflow prevention but the overall idea of this display sump is sound. If the sump sides were taller, it may be tough to get the skimmer in and out.