I'm pretty sure I figured it all out.
The canonical version of Donnie Darko is to watch the theatrical cut but to be aware of the Director's Cut. I have watched them both, and I obviously dislike the DC. But being vaguely aware of it helps piece together the theatrical cut as well. But in no shape or form does the movie benefit from cutting its best song and adding additional explanation.
Donnie Darko is such a spectacular experience because it is rough around the edges.