Should a Ford dealership cover parts on my vehicle under warranty that were modified by the previous owner?

I bought a 2012 Mustang GT from a Ford dealership about 3 months ago and the car now has a klunking noise coming from the rear that has been determined to require a rear differential rebuild to fix, which will cost a couple thousand dollars. The service tech is telling me that it might not be covered under warranty because the previous owner modified the car by putting in higher gears.

I feel that I bought this car from a dealership, still under warranty, and had no idea about the modified gears, I shouldn't have to pay for this rebuild myself. Thoughts or knowledge?

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