You are not going through customs because of where you are going. You are obligated to customs because of your ship. Once you board, since it is NOT US registered, it is like you are going to a floating foreign country.
The Passenger Service's Act, is the reason for the foreign port stop of Victoria, makes no difference if you get off the ship or not. If you want to avoid customs, then you must take a US ship. So yes you will be going through customs in Seattle.