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Yes, they'll deny anything.
Warranty works by 1) you having a problem that is covered by the terms laid out in the warranty, 2) the dealer or authorized shop does the work covered, 3) the dealer or shop gets reimbursed by the warranty provider, be it corporate office or 3rd party fancy warranty company.
If anything on your car prevents #3 from happening, #1 won't happen. Dealers and warranty have been around long before you and I were born, they blanket deny claims initially to cover this.
Usually people with mods only push through a warranty claim if they can overwhelmingly convince the dealer that it is covered. Only the dealer that cares will do work for you, most don't care about modded vehicles and flat out show you the door.
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