Yes, qt support was added to 2.2 or 2.3(I forget, its been a while). So this was a pre-Apple aquisition decision(everyone assumes that Apple did this). I'm purely guessing here, but I assume it has to do with the constant interaction compositors have with files outputted from an Avid edit for matching which back then was 99% quicktime since windows based avid solutions were brand new at the time and still very buggy.
Just use quicktime, it works just fine. There is a mpeg plugin here on highend, but it isn't a great solution unless you just want a delivery format for the client that everyone is guaranteed to be able to read.