If you are not removing the window trim yourself, but having a shop do it, there should be no problem. First i would take the car to another shop as it sounds like the one you mentioned is not qualified. The trim is attached to the car just like a Mercedes vehicle. Tell the shop that, and there should be no confusing or problem. It is a simple routine job at every windshield replacement garage in the country. Just be certain to tell them if a clip comes loose from it's adhesive to reattach it with new two sided tape. THE FENDERS SHOULD NOT BE REMOVED!! That's ridiculous.

I removed the trim pieces two years ago and painted them myself. I removed them from the glass side of the clip, but they my come off easier by getting under the top center trim piece from the roof/painted side as a previous poster mentioned. Remove the long roof piece first then the two side.