The diagnosis seems plausible. But I'm not clear on why they are denying warranty coverage. Your turbo should be covered. However, the aftermarket intake might be what they are laying this on. Unfortunately, if they want to be *********, they probably got you on that. Even though I don't believe it caused this problem, and those turbos are known to gunk up and stick.

If I was paying the bill, I would pull it out of a Ford shop and get an independent second opinion.