In my opinion, virtually all the horsepower gain is in the tune. Like you, I have seen dyno results of cars with just a tune, and they show the same 15-20 horsepower that the folks with "CAI" get after a tune.
While it is possible that the factory left 5-10 easily obtained horsepower on the table, it seems unlikely, given the expense they went to in modifying the engine for the '05.
If the gain from the CAI is really less than 5 horsepower (as I believe to be extremely likely) than it is an increase that could never be felt, but could be measured at a dragstrip. As for the folks who can "feel" the increase of 5 or 10 horsepower, well, the placebo effect is a real phenomenon. A two or three percent change is not perceptible without instrumentation.
Having said all this, my '05 is completely stock. However, I did spend 19 years seriously modifying a fox body.
Owner1