I see we are getting somewhere now..
1. Nope, at least not with 100% certainty that it is the way the PCM is calculating it. Mostly cause it could be referencing values in a number of tables most of us cant even see with out tuners yet.
2. If you leave the MAF plugged in, how do you know the PCM is not using the maf for not just spark calculations but fueling as well? And then, when you unplug it again it switches to calculated values based on VE that come out completely different then the MAF based calculations and as a result commands different timing?