Perhaps the easiest solution would be to install multiple instances of minera, with each instance launching cgminer/bfgminer on a different listening port for the api.

On the new Rboxes, I've run 10 units off of one raspberry pi using cgminer main and the rockminer fork on minera. The only thing I've noticed is that the main branch of cgminer can't handle starting up with more than a few units at once. You have to start with 4 or so, then plug in each subsequent one individually.

Duplicates are an issue with BE200 chips. They won't affect your hashrate as it's just submitting a share twice about 10 percent of the time on average. This should not alter the amount of work being handled by the rbox.