Depending on how cool you are with your dealer...Like Narcissus said most mods will void your warranty so if you can't take it off without it being noticed you stand that chance...We've got a cool dealer here that takes pretty good care of us and will submit for warranty repair mods included in most cases...
Small airbox mod... if ya leave in the flapper valve, you should be okay.
Exhaust... no biggie
Pair valve mod... that could void warranty on the powertrain.
If you are that concerned about your factory warranty, don't do the pair valve mod. Not that big of a difference to begin with considering your initial mods. Do that one after the warranty expires.
Keep in mind, if you go in for warranty repairs, make sure you remove/replace any related mods.