First, let me apologize for getting into this thread late.
Second, I just went through some of this bizarre garbage when I moved to Virginia and took my KB MM to a new dealer. The Service Manager wanted to void the warranty on the whole car, after disassembling it and refusing to work on it (although, nice guy that he is, paid for it to be towed back to my home) (sarcasm intended). Then he started the paperwork to void the ESP (based on his conclusion that this car was a "dangerous car" and should not be driven).
Making a long story short, I called Ford customer service (the number's in the Owner's Manual) and made a verbal complaint, and then learned from them the web site where I made a written complaint against the dealer; naming names and so forth).
About a week or so later, after I ended up getting the car fixed at a non-Ford repair shop, I get a call from the Zone and another one from the Region. They met me at a different dealer (who is now my 'dealer of choice' in Virginia) to inspect the car and review the offending dealer's actions.
At the end of the day, (1) they told me they had never seen a car as well maintained as mine, (2) the ESP was reinstated with full coverage; (3) the out-of-pocket repair costs were reimbursed, and (4) the offending dealer was written up*.
My point being - don't accept what the first dealer says; he ain't speaking for Ford. He's only speaking for his own dealership. Write him up if you think you were mistreated, and then find out which dealer in your area is more receptive to modified vehicles, and then take it over there. You'll probably get better treatment. I did.
* : this is important at holdback/incentive time, because a write-up will get those payments reduced.