The only reason at the moment is that my soundcard & playback software isn't setup to stream out ac3 in avis to my amp, meaning if I were to make an avi with 5.1 from 2.0 source it would follow this line:
2.0 source upmixed to Pro-LogicII 5.1 AC3 during creation, playing the avi back the software would downmix the 5.1 to 2.0, then output that to my amp where it would upmix again to Pro-LogicII 5.1, instead of just sending the unprocessed 2.0 audio to the amp where it would upmix to Pro-LogicII 5.1.

If I can get my soundcard & playback software to stream ac3 to my amp I may go with the ac3 option for the XviD, otherwise I'll stick to mp3 (256kbps as that's the highest bitrate my VirtualDub can encode to)

edit: well the rough audio sync on the 4.5gb XviD file of ANH is done, time to fire up the projector and have a watch