Three things to consider, can you open the vent window, does the mirror hit the main window, and is the mirror usable (can you adjust it and see out of it). Centering the mirror in the valley may cause an interference fit, but as you figured out, the base mounted a bit to the inside will move the top out to provide clearance. It doesn't take much, maybe an 1/8 inch. Doing this will cover the first two of the three considerations, the last is a general statement. Is this a new installation, as in a replacement for a standard mirror? If so, I'm curious about what you did about the existing holes?
Jim