handbrake uses the more applecentric mp4v2 library for mp4 modifications as opposed to mp4box. with kurtnoise MIA, i don't think anyone is currently working on mp4box. so you might be stuck...
looking at the mp4v2 documentation running this would probably arrange the atoms in apple's special way, i dont know if this will save you time though
Quote:
mp4file --optimize filename
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ru setting the device type to iphone in megui?