That's not entirely true.
An STI swapped GC RS and a stock GC RS are not and should not be in the same class. The raw times cannot be compared in any way.
Pax times are the only thing that can even out any two dissimilar cars in any reasonable way. Additionally, the levels of each class are important. A Corvette in Super Stock and a WRX in D Stock can't compare raw times though they are both stock. The comparison can only be made after the respective pax factors are applied.
A properly prepared car (to the maximum of the rules) will, on paper, be faster than a car that has NOT had all the available mods done to it that are possible. However, when you add in the drivers skill, or lack thereof, anyone can be faster on any given day. A good driver in the stock GC can, and probably will, beat an inexperienced driver in the swapped GC. In Pax times. Which is how points and awards are determined. Raw time is only for bragging rights. The swapped GC may get better raw times. Duh, it's turbo charged and has STI suspension. Of course it's going to go faster.
In theory, Pax factors take the car out of the equation when trying to determine who is faster. A car that has not been prepped to the max of the rules will, in theory, be slightly handicapped, but not to enough of a degree that it will actually matter. The drivers skill is a MUCH bigger factor.
In autocross, the rules are the rules and it is your own responsibilty to adhere to them. "The Club" does not carry out inspections to make sure you are in the class you are supposed to be. Nobody is going around looking at what everybody else has and making sure they are in the right class. Maybe at the national level people are, but not here locally. But if you have a turbo car (that didn't come from the factory that way), don't flip out when someone tells you that you can't be in the stock class. More than likely, they are just trying to help you out because they know that you probably don't know all the rules. I don't know all of them, I know some of the big ones, but there are too many to be familiar with everything. Last event, I told someone they should be in Super Street Modified and forgot that SSM is for two seat cars only. Oops. Timing/Scoring caught it.
If you want to whine about the SCCA rules, there are other clubs and other types of racing which have fewer. Not NO rules, just fewer. The New Hampshire Sports Car Club does simpler classing (race tires+Race car, Street tire+road car type classes). And Rallcross has classes based solely on FWD, RWD, AWD and tires.
And Dan, don't even try to tell me that you had to jump thru fewer hoops to get your car into a big boy rally than for any autocross.