Is DEQX a game changer?

The logic behind my response is that DEQX corrects the speakers (+ Amps) & room whereas the QOL appears to deal with phase anomalies on the source recording. Adding this component between the Premate & amps will upset the measured relationship so I would not do that. 

"Thanks, If the QOL is placed before the DEQX Premate would I need to run the measurements again?"

No, the DEQX processor measures the effect of the speakers/cabling/amps downstream & the QOL is going to address source material upstream. This has nothing to do with in-room measurements.

The PreMate microphone measurement is based on a rising frequency plot created by the processor & will have no correlation with anything beforehand in the rest of your system (which is the correct way to do this).

Then, during normal listening, it will be fed a ’corrected’ source signal & it will phase & time correct everything for the speakers & room afterwards based on the chosen calibration.

.....If you added it after the PreMate (especially if you then took a measurement), the two separate phase corrections may give strange results & it’s definitely not as DEQX intended.

Yes those confidence levels should be fine. Only 3dB between L & R main speakers means your mic was fractionally off centre so look at the impulse response of both in one viewer window, zoom in and take the mid point timing as the reading. (It will probably be no more than 1 or 2 fractions of a ms difference between the two main peaks & only really visible at a high zoom level).

The best way to set mains to subs is first to align the faster sub (usually nearest to your listening/measuring position) to the slower sub, then align the pair of main speakers (average reading as above), also with the slowest sub.

Finally, take another measurement afterwards to verify & you should see both subs initial peak at the same point & the main speakers main peak now also at the same time alignment. I always find it best to open two viewer windows, one for the pair of mains, one for the pair of subs. If you try and see all 4 measurements in one viewer, the scale usually makes the sub measurements look almost flat and impossible to interpret accurately.