In a court of law, you could probably win. The BHAF is made by Fleetguard, and I believe they rate as having the same efficiency as the stock air filter. If you have oil analysis done once or twice, you would then have scientific evidence on your side showing no air filtration problems. The stock air box is probably more likely to leak around the filter, so the BHAF probably is equal or better in protection (my guess, not proven fact).
BUT - if your dealer denies a warranty claim for say, $300, or even $1500, do you want to potentially spend thousands in court just on the principle of the matter? No, you don't, and some dealers will use this to their own advantage. The good ones won't deny a claim if your mod is unrelated to what failed, but the bad ones can take you for a ride.
It all boils down to this: Some of us have decided to make selected modifications, in order to make improvements to our trucks.
BHAF = Fleetguard Part Numer AH19037.