Have you already built your sump?
Are you going to be running a manifold?
If you haven't built it and you are going to be running a manifold, I'd make your frag section the first chamber and plumb a line off your manifold.
I was playing with the same idea for a low flow refugium.
Here is a crude sketch I drew to explain it to someone. Just change our fuge for frag.
I bet that would solve your water movement issue. But there may also be easier routes for you to take.
Otherwise, The only problems I see are potential pest introduction, algae growth from the light in the sump, and addition heat transfer to the system.
That being said your frags are acclimating to the water that they're going to be put in long term, so there are definitely benefits beyond frugality and compartmentalization.