Actually you want to speak to your dealer, they are the ones who will give you a hassle or not.
Generally speaking, if the aftermarket parts are not involved in the problem being fixed under warranty, then it should be OK. But that leaves a lot of wiggle room. I would think the items you are interested in should be fine, as their presence is unlikely to create problems, but their installation could be used against you (installer messed up something during the install, etc) in the future. YMMV