I think you will be ok with an exhaust system. I wouldn't worry about the BOV, you can always swap it out if you need to take your car in for service. I had a 98 R/T, that had intake, header, full exhaust, solid motor mounts, bobble strut, MP computer, underdrive pulley, ext. And I never had any warranty problems. It really depends on the dealer, and whats wrong with your car. If an aftermarket part effects the part off your car that needs service then it will void that part of the cars warranty. Like I said though I think the exhaust and BOV are safe.
Ryan