Media Server :: Tool To Rewrap / Encode To MP4 Or F4V?

I have tried countless times in finding out from Adobe what would be the best solution to use the already 100s of videos encoded to H.264 in the mp4 container. Unfortunately, salesmen never know the answer yet keep asking me to buy. What benefits, if any is there to encoding to F4V over MP4 other than the ability to inject metadata without having to use a sidecar xmp file like you would if using MP4? The only downside I see with going F4V is that files will not be playable on set tops, gaming consoles, and also iPods.

Does FMS protect files already encoded to MP4 and if not, is there a tool to rewrap the MP4 into a F4V? My overall goal is to be able to put all metadata needed into the file and use actionscript 3 to populate the information on a web page and in the future an AIR app. I would love to pull the trigger and buy FMS but it just seems like the salesmen are reading from a brochure and never once address my questions let alone find me answers.