You didn't get any real answers and I just came on the site for the first time in weeks, so here you go.....
I have tuned my car both ways. However, with twin turbos and not an SC, the tuning would be a little different but the same in principal.
If your MAF does not hit its upper limit or "clip" up to your engine's maximum HP (in other words it is able to meter the air coming in up to the maximum amount your SC engine can ever stuff in there) then you are fine to tune with the MAF. You have sort of limited control over AFR under boost because none of the tables in the MAF tune are able to be adjusted when the manifold absolute pressure (MAP) goes above ambient air pressure but it can work OK.
In my case, the MAF hit the upper limit at just over 4K rpm and my tuner give me my car back in a nearly un-drivable condition and said there was an experimental new MAF that would get me to 6K and I said "no thanks" and took over the tuning myself. Problem is once the MAF is done there is pretty much no way to properly control AFR after that point. And no way to manage the transition between where the MAF is working and where it is not working.
So I got the HP Tuners 2 bar SD operating system installed a wideband O2 that logs data in HP Tuners and did my own tuning and could not be happier.
You download the new operating system, install it, pop in a $79 GM 2 bar MAP sensor in place of the old one and then just go to town. The big advantage is that the new system meters fuel based on MAP and you have complete tables to work with that cover the range from full vacume to 15 psi of boost including the VE table and a separate boost-only table that allows you to depermine what AFR to use depending on whether you are on or off boost at any RPM and throttle setting. Plus you get to determine when that boost table is selected.
I have been running my SD tune for a year now and the car runs flawlessly. It is definitely a time-consuming exercise to get the AFR dialed in for all conditions but worth it. HPT even gives you an AFR error table that makes the job a lot easier. Finally, when all done you can still turn on long term fuel trims and closed loop operation via the O2 sensors in order to get that perfect AFR and fuel economy while cruising around.
HTH
