Unfortunately, most of my tuning experience comes from tuning LBZ ECMs. I haven't really looked at many LB7 or LLY ECMs and I have never looked at an LLM ECM, although I would guess it is closer to an LBZ than an LB7/LLY. Because of that some of my observations may be different than yours, but here's the way I see the chart flow, how they fit together and where mm3 fits in.
You start off with the torque reference to throttle position where your y-axis is throttle position, your x-axis is RPM and the data entered in the table is your torque reference number.
From there you go to the mm3 to torque reference number where your y-axis is torque reference, your x-axis is RPM and the data entered in the table is fuel in mm3.
From there you go to the base fuel pressure table where the y-axis is mm3, the x-axis is RPM and the data entered in the table is desired fuel rail pressure.
Now that you have your desired mm3 and your desired fuel rail pressure you can go to your main injection pulse table where the y-axis is fuel quantity in mm3, the x-axis is rail pressure and the data entered in the table is pulse width.
Now, theoretically, when stock this table should be accurate for how much fuel the injector should flow at x pressure for y duration. I believe when you log the main injection fuel quantity this number is shown based solely on RPM and tq. ref. If you leave the injection pulse table stock then the mm3 should be accurate, but when you change the pulse table the mm3 number is no longer going to be accurate and will only be good as a reference point in tuning.
Okay, lets say your tq. ref. number when cruising at 2000 RPM is 300 ft-lbs. Now lets say your tq. ref. table calls for 30 mm3 of fuel at 2000 RPM with 300 ft-lbs. That table has no idea how much rail pressure or even what duration is used when you are at 2000 RPM and 300 ft-lbs. If you are cruising at those numbers it will report 30 mm3 regardless of any other factors. Now if you have your pulse turned up so that it is injecting too much fuel and you have to back off the throttle, reducing the tq. ref. number, you may log a lower fuel quantity, but it isn't becuase of anything to do with your rail pressure, it is because you screwed up the pulse table and it is no longer accurate consistent for the quantity of fuel delivered in a given amount of time at a given pressure.
Now that I've said that, I know there are tables that add or take away from main injection pulse for certain positions or limit maximum quantity for different conditions, but I ignored those for simplicity's sake because, from what I've seen, those tables would have the same effect no matter what your rail pressure or pulse time is. They are usually things like ECT, IAT, Barometric Pressure, etc.