It seems like this always depends on the situation/shop/company/adjuster. On my previous car with mods (tune, exhaust, wheels, coilovers, etc) I had an aftermarket warranty and the adjuster that would get sent out would literally just look at the car, ask the tech what's wrong and approve the work. However, if an adjuster came out that would make note of all of the mods, they could have denied the warranty claims I made. I was also friends with my dealer, so they wouldn't mention the mods.
It's really a hit or miss, it just depends if you want to take the risk of potentially getting the claims denied.
Also, if they don't like the quote they can negotiate with the dealership on labor hours. On one of my claims they approved 3 hours less than the original labor estimate.
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