I don't think that bundles are flawed at all (in as much as we can rely on any binary-packed format -- which we do A LOT), but if I have one comment it would be that there is a void of information about the construction (i.e. the spec) of bundles or a desire to have a diagnostic or repair tool to help recover from a situation where things go wrong. It's not like the folks who wrote Sonar are hiding these details; I just figure that most times nobody cares so long as nothing goes wrong.
Years ago when I was more active on the Cakewalk forums, maybe 2006 or 2007, I could swear there was a detailed thread about bundles and the same kind of issue I'm experiencing now, where Noel himself gave a basic breakdown of the composition of a bundle, how it's basically a gigantic RIFF WAV, how padding is used in the data sections, and so forth. I keep trying to Google for Noel's detailed response but I'll be darned if it I can find it when I would really probably find my answer just by looking at it. :-(