One could maybe implement some pre-fetching of work and caching of nonces functionality to add the potential 12MH/s - but at the same time maybe the FPGAs need this small idle time to cool down a little bit.
Yes, I also wouldn't worry too much about tweaking this inefficiency out. If a non-throttling 816 unit throttles with 832 firmware (a 2% increase), then that same 816 unit would likely throttle if the 80ms idle time was eliminated.
On the other hand, there's a number of us who are running 896 in cool environments are getting 883 MHash/sec without throttling. Until BFL releases even faster firmwares, we could benefit from this improvement.