Ironed out Audyssey/toe-in issues after some experimentation. With with my room/speakers, the best Audyssey results is where first-measurement is on axis to all 5 speakers - or very close. Speaker toe-in aimed just behind center . One thing I should have done more of in past was spread the fronts out a bit more - closer to 50-55 degrees. It's tricky with room and keeping away from sidewalls - but first reflection point will be 3-4 feet away no matter what. Kept microphone at tweeter level for fronts - which is ear level too - and keep mic at LEAST a foot from couch. Not toeing in fronts causes too bright a result in this room, perhaps as it's trying to overcompensate to reach the center spot (per FAQ), and reflections. But the toe-in and ear-level measurement were important to working with the room to eliminate the brightness, eliminate reflection best as possible, and flatten response. The subwoofer has been modified, and the area treated - so the lower-region is as tight as it can be.
The problem I was facing was a non-existent lateral soundstage when using the toe-in, especially sitting a few feet to the left off-axis. It turns out it was a mild bass hole from the mains i was missing. Upping the crossover to 100z filled in a mild hole the Energy C-100s weren't producing at 80Hz. (Audyssey crossed them at 80Hz, but the sub does a touch better job for just that 80-100 range). Granted I have all rear-ports of speakers plugged, as that is the right move for their locations. For the main L&R though - needed just a touch more fullness for their location. Unplugging-foam from the mains would do the trick but having the sub, with far more EQ filters, fills in that small region much more efficiently. Can't localize that bass if I tried. Result has been best I've ever had. I use Dynamic EQ as I have for years - LFE or bass has never been overinflated since the bass was set up correctly. Volume is within 10dbs of reference before it gets overwhelming, which isn't bad for an apartment (never disturb neighbors more importantly).
There is still some mild room-reflection, can tell by some ear fatigue. But it's still a much more pleasing sound than before. I credit the Denon X1000 for a lot of it after meeting it halfway.