Looks beautiful. I would say it's the room, and the fact that rear firing port could possibly be reflecting off the wall on the left and the right isn't but I would say it doesn't matter too much to loose sleep over it. How does it sound? Are you considering room treatments? Those may help on the wall. You can't do much to fix the timing of anything in your yamaha setup, you'd need external equalization. Something like a MiniDSP. Their FIR filters correct phase shift or something like audyssey. But here is a way to do it for free if you use jriver for streaming https://yabb.jriver.com/interact/ind...?topic=87538.0 The best control you can use to correct timing alignment in your setup is the sub phase control thats the only one you can use to align with the mains.. or moving the speakers/furniture/listening position. Like moving the sub to the right and shift the speakers and entertainment center left?
I found Time-synchronized measurements can be performed with a USB microphone using REW's "acoustic timing reference" feature. To enable it, go to the Analysis tab of the REW Preferences dialog, and in the section labeled Impulse Response Calculation, make sure the Use Acoustic Timing Reference option is chosen before making measurements. This requires REW version 5.15 or later. but if one is using HDMI there are other factors to consider check out http://andyc.diy-audio-engineering.o...ring.html#holm
I would say if you take mulitiple measurements and the phase readings are consistently different then you might not be able to trust them.