I got my Pilot back from dealer. The paint job was OK, and if you are not specifically looking for it, you would not be able to tell the difference between paint and the vinyl tape. However, they bent the side mirror molding when they did it. The dealer said it was "within tolerable range," and does not want to replace it.
Meanwhile I also notice another window frame developed bubbles as well (not as bad as the first one). Now I am reluctant to take it back to the dealer, fear that something else may be screwed up by them.