I was just going to say that with MR you can have problems with alpha channels if you dont set it up correctley.

I have used the alpha in a AVI file but i'm not a big fan of it as I have had problems with it in the past with some softwares. (with After effects to be honest)

I personally render it as a series of TIFF's and let aftereffects import it as a image sequence, and I have had to date no problems so far.