This is an interesting discussion! I've found the whole issue of delivery formats quite unhelpful - my media player, for example, can't play 5.1 AAC so MP4s have to go through a conversion to MKV/AC3 before I can use them (and the fact that MP4s can't - or at least don't - contain AC-3 raises some issues regarding preservation).

Since I'll be turning out a couple of projects shortly I'm also concerned with the formats I should be packaging my stuff into for the best results - I could of course just produce VIDEO_TS or BDMV folders for burning, but I'd like to think we're getting past that now.

Anyway, I've started a thread here in case anyone has any thoughts they'd like to contribute!