I'm going to say it really depends on the dealer.
On my 2004 GT I put in a set of Steeda under drive pulleys. About a week later my CEL came on, and I pulled the code (P0340) - camshaft position sensor. I took it in and it was somehow related to the alternator (aparently this is a common issue). They put in a new alternator for me even though there was clearly a different intake, throttlebody and set of pulleys on the car, in addition to being lowered & having a Cobra R front bumper.
If you have the capability of doing the install yourself, just do it. In the slim chance that something catastrophic happens to the car/engine, you can swap the stock ones back yourself, though it would be a pain to do so.