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vlc uses an own mp4 lib which was mainly derived from their own .mov lib (i think both are still very closely related in the source)
for example vlc already can produce text streams inside .mp4, but simply places them in a way as defined for .mov and not as defined in mpeg-4 part17 for .mp4
the .mp4 muxing in vlc is mainly developed by fenrir, a dev who also wrote the x264 gpl codec and now works for the ateme corporation (which devs its own .mp4 solutions). as the work on the vlc mp4 implementation by him has basically stopped since fenrir joined ateme (like his x264 work), i think it will not be fixed soon...
So maybe this was derived from the existing QuickTime4Linux and/or early OpenQuickTime (= 3ivx) libraries. Anyhow, thanks for the information.