No, you will not lose the MAF...
with a COS you can still run the MAF...
the problem with the MAF in general is that larger boosts may exceed the PCM's MAF limit (512 g/s)... this is an internal limit of the PCM used on Gen3;
[ to avoid hitting this MAF limit, you would scale down the MAF, VE and IFR tables (and achieve the correct fueling) ]
The V1 interface had 3 license levels: Personal, Commercial, Workshop; an upgrade from Personal to Commercial was $50.
The V2 interface had 2 license levels: Commerical and Workshop... i.e. when you purchase a V2 it already has Commercial level.