1: If it's using the MAF, it won't use the VVE under boost conditions.
2: and 3: It all depends on what the exhaust AFR is. Commanding specific ratios does not actually mean that's what the engine is using. Stick a wideband in the exhaust and see what the engine is really using.
3: Command torque is the way of the future. The ECM maps the pedal position to a "desired torque" value. Then it uses the torque estimation tables to work out how much throttle is needed to proved the desired torque and opens the throttle to the required amount. This is good as it allows for changes in fuel types (spark blending moving from high to low tables), barometric pressure, air temps etc. So it makes the car feel more "constant" over a wide range of operating conditions. It's bad in that it messes badly with modifications as the torque model changes with each mod.

Without seeing any log data, I'd suggest that the ProCharger tune is a "base" tune and is meant to be a starting point for more work.