I do believe the ford emblem can be removed from the trim, BUT it is a pain to do so. The trunk trim in general is pretty annoying to remove for the purpose of wrapping. There are multiple, *fragile* clips, and I believe a few screws. The window trim is also annoying as it is a very thin material and can be easily warped/bent out of proper shape when removing. It isn't too expensive for new from ford, which is good, but it is a lot more than I would want to spend on extra parts for wrapping.
That said, a pro most likely will have experience. I plasti-dipped my SHO and it held up pretty well until the car got totalled.