It could be improved...
Here's my use-case. I record mono guitar tracks (guitar directly into interface) and do all the amp/fx work in the box (BlueCat Axiom). I normally leave the interleave at 'stereo', because I want the stereo effects done with Axiom to play back in stereo.
At some point in the process I usually do the AudioSnap thing to clean up my mediocre playing. Once I've got the timings straight, I want to render the AudioSnap using the offline Elastique Pro. I bounce the uneffected guitar audio (channel format mono, the only ticked box is 'fast bounce') to another track, delete the original recording, and move the bounced clip up onto the track with the amp fx. As I never listen to the raw guitar recording without going through the amp sim, I hadn't noticed that it was boosting it by 3db. Though at some point I thought "hey, the track is a little 'heavier' than I remember it being".
Thanks to this thread, I discovered that if I temporarily set the interleave to mono, do the bounce, move the data, and then set the interleave back to stereo, everything works as it should - no additional 3db of gain.
A bit cryptic, and not what would be expected given the settings in the Bounce to Tracks dialog, but at least it works.
Maybe a pop-up "You know, this is going to boost your recording by 3db" dialog box should appear, along with a "yeah, I understand, don't tell me again checkbox" for those who know about it.
If the semi-bizarre behavior can't be changed without breaking a bunch of other things, at can at least be documented (in the app itself) to avoid the gotcha to new users.