Here's the way I look at the subject of acceleration potential, based on the info presented and my admittedly limited knowledge of how these engines work:
At high altitude, my n/a engine will have less air available, thus lowering power. A WRX will not be affected as severely due to its forced induction. As altitude increases, the disparity between the two is going to widen and the n/a engine will lose more of its ability to accelerate, thus rendering PAX factoring inaccurate. This will undoubtedly affect other cars differently, but I think that the RS and WRX make a good example due to their similarities.
The subject of the ECU altering timing is a good point, but it's only advantageous if the car is driven regularly at the course's altitude. Going from Carson to Stead is no big deal. But driving up to the Tahoe area from Carson creates a noticeable decline in my car's power output. If I simply drive my car up to Squaw the morning of the August autox event, will my car have time to acclimatize itself to the altitude before I take my runs? Probably not. Normal aspiration FTL.
Of course, I ultimately fall into the "so what" category - I'm a noob to racing, so the fact that a WRX will retain a better percentage of its power output than my RS should not be my concern, nor should worrying about my PAX score or inequities in the factors. My focus is just working on my car and learning to drive faster.
And we've had this discussion before - we're autocrossing for fun, paying minimal entry fees, and there are no real repercussions or rewards for losing or winning (unless you're going National, I guess). Sure, genuine effort should be put in to making sure events run smoothly and safely, but there are too many people taking it too seriously. I'll bitch half-heartedly about Cody having a better car for high elevation, but I'm certainly not going to demand that we launch an investigation into "fixing" PAX factors. I'll save that for the crotchety old-timers.
And if it really mattered, I'd have a different car!