People have gotten bad axles out of the box before that cause vibrations, that sounds like the issue here as well. I hope they sort it out with minimum fuss.
I get what you say about them putting in a non-oem part without notifying you first. When our MPV was a few months old, we got a crack in the windshield, and I got a quote from the dealer over the phone and it was about $100 more expensive than an auto glass place iirc, so I went with them. I got the van back and went to adjust the rear-view mirror and it came off in my hand. I pushed it back on but it would just keep coming off. I took a closer look at it, and the mirror base on the windshield was smaller than required for my oem rear-view mirror, and not only that, but the installer tried to make up the difference by caulking it in place with the black urethane(?) that they use to install the glass. I was livid...this basically proved that the installer knew there was a problem and tried to pull a fast one. I figured they put in the glass for the lower trim MPV, but when I confronted the service guy, it turns out they put in aftermarket glass. This pissed me off even more!!
Same thing as was told to you, he said oem glass is too expensive and they always put in aftermarket glass. I told him if I wanted aftermarket, I would have gone elsewhere! At the end of the day I paid a little more and got oem glass and the dealer paid the installer to re and re the aftermarket glass for the oem one.
1997 MX-6 LS