I've looked over the dyno charts and comments by anm6 and MS3JamOnIt, and talked to anm6 via phone a bit today. Here's my observations on their dyno pulls.
Air/Fuel Ratios: The air fuel ratios they are seeing are in line with what we got on our car. Actual stock AFR's at wide open throttle, above 4500 RPM, are in the mid to low 10's, and can dip into the 9's. This engine is is different than most engines, and tunes, that dyno shops are used to tuning. It is direct injected, so the fuel atomizes a lot better than with a port injected type engine. There simply isn't any issue with the cylinders washing out or causing a misfire or dropping spark with our tune at WOT with this engine. I can elaborate further if needed.
Air/Fuel Ratios with "Stock" Tune: The AFR's staying in the 11's with the "stock" tune are actually lean. This is being caused by an incorrect MAF calibration. With the stock air box and stock tune, your AFR's would be in the 10's at WOT. When you install an aftermarket intake, and don't correct the MAF calibrations, the stock tune is going to lean out at wide open throttle. The computer will correct the AFR's at part throttle with the fuel trims, but at wide open throttle, the ECU is adding the amount of fuel based solely on the air and load calculations from the mass air sensor. Running the aftermarket intake with a correctly calibrated MAF sensor with the stock tune would result in AFR's in the mid to low 10's at WOT.
Dyno Testing: One of the critical issues when dyno testing these cars is heat soak. With the intercooler being mounted on top of the engine, it is easy to get heat soak between dyno runs. The trick is to maintain consistency between the pulls. When you start seeing power drop off between pulls, then you're probably getting some knock retard. Even a slight bit of KR will reduce power output considerably. When we were tuning our car, we had to fabricate a bracket to mount an axial fan directly on top of the intercooler to keep fresh air coming through it. Here's a pic of it on our car.

If you make back to back pulls, and your power numbers are off more than 3-4 HP between them with no changes, then there is something else going on.
Having the hood up and the fan on the car might not be helping that much. A lot of dyno shops have the rollers to the rear of the bay, so that the front of the car is facing the bay door. They can put a fan in front of the car, and blow fresh air across it. If the front of the car is facing the inside of the shop, then its likely that the fan is just circulating the heated air. The radiant heat coming up from the engine compartment is being blown around by the fan, and is just being sucked in by the engine and intercooler.
Power Gains: Something else to look at is what RPM you're starting the dyno pull. With these cars, you need to start the pull as low of a RPM as you can. If you look at our dyno chart, we started ours around 1100 RPM. This allows the turbo to spool up to full boost. A 2 wheel chassis dyno doesn't put the same load on the engine that is on it when you are driving down the road. The rollers are a lot lighter than the weight of the car, and the RPM's come up a lot quicker. This is what is causing the torque numbers to be lower than ours.
Our max gain was made at a higher RPM than peak HP. The main benefit of aftermarket air intakes and exhaust mods on these cars is the improvement of airflow at the higher RPM ranges. The Hypertech tune takes advantage of the added airflow up top, and the numbers show it, even on a stock vehicle. You should see significant gains over stock from 6K up.
I suspect that both cars were experiencing some knock retard, although anm6has a front mounted intercooler, and let the engine cool down quite a bit between runs. I suspect that he was getting some KR due to the MAF calibration being off.