Well, ain't that a thinker.
You're looking at features or parameters that my simple setup doesn't include, so I'm out of my depths here. I only have one VE table. That said, once you actually get things put together and start tuning, the effect of those will start to become clear.
You're going to run leaner than 12:1 at economy cruise, aren't you?
An aircraft application has some advantages in that the throttle position, load, RPM, and temperature are far more static and have far narrower operating ranges than an automotive application. Acceleration, throttle response, cold drivability, etc, are non-issues. So you won't need to worry about them the way you would on the ground. That may justify simpler hardware and firmware than you are thinking of.
An IO-360 is already injected. What are you hoping to gain by going to MS?