I've hard both sides of that story. I've heard certain companies care and others don't. But like somebody before on here if something goes wrong they have to prove it was done by the AP, which will be extremely hard. They still have to cover the warranty, at least that's how I had it explained.
And remember--Ford has (a) more money, (b) more time, and (c) more lawyers, as well as (d) more money, (e) yet more time, and (f) always more lawyers. If Ford views it as in their interests not to hold to the warranty for some reason, all they need do is drag things out, and at the same time isolate the plaintiff and plaintiff's issues, making it seem as if this is a special case solely happening to someone who modified the car in ways so as to stretch its capabilities, etc.
Now, this all said, everyone should always remember that anything that sounds like legal advice on a forum like this is probably worse much, much less than what one pays for it.