Only problem I have found in leaving the MAF and using PE is big weather or altitude changes. Once everything is dialed in with LTFTs during idle and part throttle/cruise its all handled by the MAF so it will compensate for weather/altitude changes just like stock. But WOT over 4500rpm is through the PE though, if I leave the 65 degree 9.70 tune in the car and run it on a 100 degree day I'll lose 2-3 tenths because the car is rich. On the street thats nothing with a 600+rwhp car, but if I'm at the track I can log a pass with the wideband and adjust the fuel pressure or PE table to lean it out and pick it back up some.
Only downside is if you tune the car lean when its hot it will go way too lean when it cools off or you drop in altitude a bunch because it needs more fuel to make more horsepower and nothing will compensate since the MAF is way maxed out. Works for me anyhow
With a 99+ car I would no doubt use one of the 2-3bar tuning solutions out there, having a 98 I'm kinda stuck though