I was taught that a NA engine VE is usually on the close order of 70% for a very efficient engine, one with high compression and helmholz tuning. I'd make your base non-boosted engine about a 60-65% VE. I'd make the stock 3.0 about 65-70% with the tuned intake.

My concern with the MAP was thus. You have a fixed voltage range for the sensor outputs. If you spread 4bar of readings over that 5 volts of range, you get half the resolution of a 2bar sensor over the same 5volts. As you say, the ego is an autocorrector, and this may not matter at all, unless you get a false map of MAP values as a result of the low sensor resolution.

I agree the sensor readings are all relative. The system reads the system voltage and does a correction to give repeatability as the battery voltage varies over time.