I think you left out that FLV is also h.264.
I am not sure why F4V is not supported, but I am not sure it is really needed either as HD video can easily be achieved in either FLV or MOV. In fact, FLV format can handle everything F4V can and then some, while F4V is limited. Until MediaSignage supports it,if they ever do, why not use FLV?
So far I have not found a benefit of F4V and just checked again on the internet and cannot find anything to say different. F4V has been around for awhile and has not moved to the forefront as of yet and may not ever.
I would be curious as to why you like f4v over fly. Maybe I am missing something.