I Exported some audio as an .aif last night. I imported it into my Premiere Pro timeline and watched the audio levels peak/red out and sound crunchy, when they weren't in After Effects. Thinking, "I did this right and the levels aren't hot.." I tried Rendering instead of Exporting and made a no-video audio-only Quicktime. THIS time, the audio was fine when I brought it into Premiere Pro, no clipping, no hot crunchies.
I did nothing different to my audio file between Exporting and Rendering. In theory, shouldn't the results have been the same? Why did they turn out different?
If you think it's a bug, it's a bug and from your description it sounds just like that. Presumably the standard export tries to do some odd normalizing which QT does not (or vice versa), but in the wrong direction... I'd re-check your export and render settings just to make sure you know the exact details when you write that bug report. ;-)