So the easy solution you already found is to convert it twice. One time for the TV, one time for the Apple devices. I can't see very much wrong with that.
I am trying relentlessly to find the right settings for converting my movie clips to a universal format to be read by both SAMSUNG TV and iPhone/iPad.
i have tried converting .MOV(recorded @ 1280x720, Data Rate = 10500 Kbps, Frame Rate 29fps) to .MP4 (H.264/720p AAC) using Handbrake, but SAMSUNG TV is not able to read the file. While the same file is readable using iPhone or iPad.
if i convert the same .MOV to .WMV (1280x720, 10500kbps, Framerate 29fps) using Windows Live Movie Maker, then the SMART TV is able to read the .WMV version of the file, but iPhone&iPad canno't obviously.