I will give this a try based on my experience with single motor.
If you have set the ESC Max and Min at about 4000 difference, say a low of 7000 rpm and Max at 11000 rpm then 1 click of the timer is about 10rpm and 0.002ms. The Firortti has 400 clicks of adjustment, so 10 rpm/click if the 4000 difference in the ESC. I use this to approximate RPM change to adjust lap time and it works as a good approximation.
For Nose up and for ESC 2, a click is 0.001 ms, so only about 5 rpm. You have 100 clicks up and 100 clicks down on ESC 2 as I recall, so you can move the RPM of motor 2 up or down by up to 500 rpm.
I think that small variations in electronics and motors account for the difference in base rpm ot the 2 setups. I claim no expertise in making that statement, just my guess. The difference does exist, so now the ESC 2 settings allow for correction or your choice of compensation.
After guessing or estimating the number of clicks, then you can (maybe should) measure actual rpm of each motor.
If you are concerned about the base rpm differences, try swapping motor positions, or ESCs to see if there is a difference, but maybe more effort than the curiosity deserves.
Fred