Honestly, I think it is insane that automakers are still trying to pull this crap. It's pretty funny that the Automaker’s Alliance even took the time to respond to this article.
But if I buy a car, I should always be free to fix or modify that car, even if it’s a terrible idea that gets me 20 HP and 11 MPG. It doesn’t matter — it’s my car. Besides, how would this be enforced, anyway? If you were pulled over, could a cop plug into your OBD port and read some checksum or something to see if the car has been modified?