Just my opinion, I don't think the sound is mechanical in nature... that is could be the sound of metal on metal leading to a failure sound.
It is harmonic noise IMO... that's it.
Since I've been following this thread, good information by the way, I've read a good deal on the topic of tuning intakes, fluted intakes, VVT harmonics and all sorts of information that is relative to the topic at hand.
To me, running the aggressive tune to compensate for the dip is simply introducing increased exhaust gases through that range that cause the effect of pressure pulses/waves bouncing off one another back and forth - which generates the raspy sound. It is the same concept behind tuned intake runners for optimal power. Hell Ferrari even tunes their flutes to give a distinctive pleasant sound - the sound we all associate with a screaming wot/v12.
To reiterate - I've not heard the noise, that is the rasp, that was otherwise noticeable post header installation. I'm running a stage2 tune that is aggressive. The engine breaths better. The engine runs/feels better. Definitely sounds better.
I don't feel the least bit worried about running the aggressive tune. My engine runs so well now that my previous urgency to Force Induct the lil FA20 has all but subsided. For less than $1500 in mods I'm kickin 200whp all in the ass on 93oct...