From what I'm seeing it's not the factory warranty but a different Ford Performance warranty. Not sure how that affects things.
I called some local dealers last week when this was announced and they either said they don't do this or they'd get back to me, but haven't heard back.
Everyone sure likes to complain about the price. 30HP and 50TQ is a pretty good gain for the price when compared to how much it costs to make power and keep some sort of warranty. I'd also rather have the warranty since these Explorers seem to have lots of problems, so this is worth it for me. If I wanted to squeeze every last ounce of power out of the vehicle I sure wouldn't be wasting my time doing it to an Explorer. I see this as simply a small power bump and I'm happy that Ford is supporting the platform, especially when it looked like this wasn't going to happen due to the rear end bolt problems.