You can try a Re-Equalization circuit that THX has, it might tame down the treble. Also, you could use the tone controls.
After all the hype about Audyssey, I found that it won't work correctly in my system and puts incorrect levels (obviously off), Incorrect crossovers, and incorrect subwoofer polarity. I finally gave up on it. I ran it once and posted a thread about my terrible results only to be attacked and harrassed so the thread was closed immediately. I tried it a different time follow suggestions I found on the Audyssey thread. Things were a bit better but levels were very obviously off, as were everything else. It really sucked and sounded so digitized or harsh or compressed, you can label it any of these.
I bypassed audyssey, setup everything manually and boy is it singing just like my older Denon AVR-3803 that didn't come with this crap.
Also make sure you disable Dynamic EQ as it will make everything sound bright with over treble. Made sound so bad, I thought I had a crappy DSP engaged.
I don't know how Onkyo is but Denon makes it very hard to disengage Audyssey. There is no global disengagement. You have to go to every input and shut it off and it's a pain through the multiple menu levels.
My living room is setup like everyone else I know and many have their surround speakers in the same place except attached to the walls instead of on stands.
Many put the center speaker on the floor (as it is even in the Denon GUI display of the speakers!) since they have larger center speakers as I.
The only determental placement is the subwoofer since it's about 1' from the right side surround speaker, in the rear of the room, and only 3' from the main listening position. However this was the only place it would fit with any type of sound quality. I do have to put it at 180 degrees out of phase to keep standing waves from entering the listening area. It also delocalizes the subwoofer and tightens it up, taking away the upper bass boom and extending the lower bass out. Without it, it's disconnected from the main speakers and is very VERY localized. Audyssey didn't help with it at all. No matter, the 2312 sounds awesome without it.
So I think you are running into 2 problems, an inherent bright speaker with a neutral sounding receiver, then the addition of bright sound that the Audyssey Dynamic EQ will add.
Perhaps some poteniometers on the horn tweeters will lessen their output and tone down the treble, along with turning Audyssey off.
I calibrate instruments for a living so when calibrations aren't done correctly, it bothers me especially when I hand calibrated the same speaker system with great results.