If you try to download youtube movie (any movie which i tried so far) with Download Master - then if you download 720p or higher, you ll get MP4 file , not FLV. Download Master emulates flash player to retrieve video , so it looks like flash player in resolutions 720p 1080p plays mp4 (not flv) too (may be i wrong).
AFAIK youtube stores video under 720p as flv and >=720p as mp4 and another batch of mp4 files for ipads which are encoded with main profile, not high.
By the way, i was not able to find on youtube 720p MP4 files longer than 20 mins ( moov data is not huge), so their smooth playing doesnt look very strange.
Anyway - ipads CAN seek smoothly mp4 files without all this shit with moov data.
And Adobe flash player - doesnt - very strange.