Since flv supports H.264 playback and iPhone/iPad also supports h.264 playback are there any compression settings that can be used to support playback on both platforms without needing to store/serve 2 files for each video?
FLV is a container format. H.264 is a video codec. Even though iPhones support H.264, they don't recognize the FLV container format.
However, the latest version of Flash is fully capable of playing .mp4 video, which is a container format that the iPhone/iPad also support.
So if you encode your video as H.264 mp4 files, then you should be able to play them on both iPhone/iPad and whatever platform you're using Flash on.