Originally Posted by Toyota Certified Used Vehicles site
We want the cars to look and feel as new as possible
The main marketing I've seen for certified vehicles is that it's barely used, or like new. Any aftermarket mods are going to diminish that selling point.
It is really just a profit equation though, when it comes down to it. As in, is the extra money they get for it being "certified" enough to offset the risk of paying for any warranty repairs that may have to make on the vehicle. A stock vehicle is easy to assess - you know the failure rates, and the est. repair costs so you can get a pretty good idea. Aftermarket parts would be hard to assess - you don't have info on the parts themselves, and you don't know if they were installed correctly. It's easier for the dealer to just say no.