Micheal Hohl denied replacing my axle grease under warrenty (is was the wrong type of grease used by the factory) because I had an exhaust and a "group B rally" sticker on the rear window.
Bet they were still better than Lithia who refused to even test my bone stock car for a known clutch issue that Michael Hohl did replace under warrenty.
IMO, all dealership service departments are shady... unless you know someone working there that you can trust, I wouldn't trust 'em to do a job straight. Hell, I'd bring my subaru to Nissan before I'd bring it to any Subaru dealer, simply because I'd trust Cory to do the job right.
As far as the intake... take it off before going to the dealer. I had the service manager at Michael Hohl actually tell me "you should have taken off the exhaust before coming here, but since you didn't, and since it's already in the service write up, I can't help you."
Also, once you take off the K&N, don't bother putting it back on until you get the ECU reflashed for it, all you're doing is leaning out the car which at the most does nothing because of our altitude, and at the worst creates a higher chance for detonation.
Also, I wouldn't put a K&N back on at all even w/ a reflash, since they use animal fat in the filter element and many people have had issues with 'em screwing up the MAF sensors. I know I had a MAF go bad on my SVX... I can't totally pin it on the K&N drop in filter I had 'cause the car had over 200k miles, but the failure was right in line with the type of failures others have seen w/ K&Ns. Plus, they really don't flow all that much more than a cheap clean paper filter, and they certainly don't filter any better.