That noise floor is pretty unbelievable, it is close to absolute zero SPL. I would believe it if it was 30-40B higher. I think someone forgot to calibrate the SPL of his microphone
Inverting right side indeed makes it all much flatter in the 100-1000 Hz region (inverted in red):
INVERTING ONE SPEAKER!?!?? Why the heck would you want to do something as crazy as that?!?!? I stared at my screen and wondered if you had completely lost your marbles, so I decided to check.
This is the impulse response of your L and R speakers with nothing inverted. Nothing crazy here, both speakers are the correct polarity. The reason you check this is because this is the ONLY reason why inverting one speaker would produce a better outcome - that your speakers have some kind of manufacturing defect where the polarity of the +/- speaker binding posts have been reversed by the factory.
So now we check the measurement of L+R with no inversion (yellow) and with inversion (green). See the obvious problem? The green measurement has a double impulse, with the second speaker offset by about 1.4ms. In other words, you are looking at a summation error.
Indeed, if we assume that the MMM is free of summation errors, we can see that your MMM correlates nicely with your non-inverted measurement ...
... more than it correlates with your measurement where you inverted one speaker.
In short: forget about inverting one speaker. It's ridiculous, and the so-called "improvement" is a measurement artefact.
There are in fact a lot of problems with your measurement, starting with the fact that the timing ref is all over the place. Like, why is the timing ref delta in the individual L and R speaker measurement 4.58ms, but when L is measured with R, it is consistently 0.02 - 0.1ms?