I cannot answer the EO Number, but you said if they made an aftermarket kit its a diff story. I just stated they did because I have it. They do not provide a tune of course, I guess that is where Whipple and KB may be wiser choices? Again I really doubt anyone is going to flag an OEM ford piece as not being original to the car.
GT500 2.3L TVS Supercharger Tuner Kit w/ 65MM Throttle Body (2007-2012)
That supercharger "kit" was only offered as "competition only" and was not 50 state legal. Ford does make 50 state legal parts, but all engine components will come with a tune that has been certified by C.A.R.B. Ford spends a lot of money getting something C.A.R.B certified and they currently offer nothing for the 07-14 GT500. Here's the current list of emission compliant parts. Here's their statement on emission compliance.
FRPP's Whipple kit was the only one certified for the 11-12. The TVS was only certified on the 2007-2010. You can look these up on the C.A.R.B. website.
This right here.