Some good observations here.
MAF sensors are finicky little creatures. In the OLD days of Fuel injection, Air flow sensors where either a flapper valve style or a heated wire. Either way, the units had a specific calibration as a unit. In the early 90's, Mass air flow sensors came in a specific sized enclosure or built directly into the Throttle body. Then a few years ago, GM started using the slot MAF sensor. These were in variably sized housings, and can be accordingly scaled in the ECM. The MAF sensors produce a frequency output back to the ECM based on the amount of air. The size of the tube/housing affects this output. This way a single sensor can be used across mutiple flow ranges/platforms. Each Engine/car type is given a specific lookup table in the ecm based on the frequency response of that MAF in a SPECIFIC size enclosure/tube. If you change the size of the tube, it will not report the actual air flow. You have to give the ECM a new adjusted lookup table to accurately fuel the engine. This is a major part of tuning a car.
Plus, MAFs are extremly sensitive to turbulance. and can give false readings in turbulant air. In the 90's GM put a fine mesh screen in front of the sensor to "filter" and smooth the air. Performance guys would always remove these, because it's a "restriction", and it actually was, but the cost was rough or unstable idle and inaccurate MAF readings.
Ok enough with the history lesson....
If the size of the intake tube is changed from what came with the car, it will cause inaccurate air readings...Period! The car can adjust for it up to a point. The GXP can adjust about +/- 35% in fueling and the NA can do about 20% with out setting a check engine light. Some cars, in certain climates and such can live fine with the adjustments...others can not and will cause problems as we've been seeing on the boards. The very first batch of Fujita's caused codes on every car. They redesigned them, but not correctly, and it's a 50/50 shot as to seeing a light.
Our Mach II system uses a 3.00" OD with a 2.87" OD....very close to stock. But even though we're off a little, we compensate for this because unlike the other intake systems, ours is a matched kit: Intake, Pipes, Intercooler, and a TUNE. The system is only sold as a kit. It would probably work just fine on a stock setup. It's certainly the closest aftermarket system to the stock sized MAF tube.