Masa, I do believe that your flute has established yet another proof!! I would strongly urge you to prepare a paper for submission to the AES. The regional convention was in Tokyo this year, which would have been ideal,but it concluded yesterday, so don't rush. The relative proportions of your flute(incidentally, in an earlier life, clarinet here), presumably arrived at empirically, certainly are powerful data. To clinch the argument, I'd suggest that you add a temporary extension to the mouthpiece end and see if they don't start yelling that they can't hear you, play louder!
On the coincidence of room modes, if the room dimensions vary significantly, the resonances should be spread sufficiently so that the overall response is acceptable(at least the testing described in Audio and elsewhere appears to indicate this).
On the lower distortion point, I haven't really seen this discussed much as a significant advantage. I vaguely recall that it was pointed out in something I read that the lower overall volume required to be delivered by the sub amp and driver with corner reinforcement could be viewed as a minor plus.
