I agree.
You should read the warranty closely. I have read the warranty of all my vehicles and they normally say something to the effect that you can use aftermarket parts, but if the part causes damage, the damage won't be covered. What I interpret that to mean is that if you use something like a K&N filter and then have a tranny problem, they have to warranty it. If you have a motor problem, they have to claim the K&N caused the problem before they can deny the warranty. If they do, then you are stuck at the lawyer level trying to prove "no it didn't" ... vs "yes it did". Not a good situation.
My impression based on living on various forums for years is that this is very dealer dependent. Some dealers are realistic and realize an intake mod isn't going to effect much, others take a very strict interpretation of the warranty and extend that an intake mod can impact wide ranging issues.
My suggestion: talk it over with your dealer. :cheers