This is something server side not template side. If you were to get HFS to communicate with another program (I believe it is possible now, been away a while), and auto transcode files to .mp4 similar to HD YouTube, before sending them to the user, then yes they would work with RAWR-Player as it is Flash based.
Just to outline, Flash can playback .mov, .flv. .mp4 and .3gp video file formats, as well as some other copy protected ones that I never bother mentioning cause they're useless lol. The basic guide to playback .mov, .3gp and .mp4 using Flash is to use H264 video codec and AVC audio codec.
Otherwise there are other options, like WMP/Silverlight, Quicktime and DIVX plugins... In the future I can see us adding a HTML5 player, but we are nowhere near that being a web standard, so we must rely on 3rd party plugins to playback video, Flash being the safest bet to reach the most people.
Oh, also this program would probably just convert and store them in the folder as playback options... I don't think it would be possible to have it 'live convert/stream' when you select an option... not smoothly anyway, HFS wasn't really built for that purpose.