Cardinal Sean P. O’Malley flung open the doors to the Seaport’s new Shrine of Our Lady of Good Voyage before overseeing the first Mass and dedicating the nautically inspired church with smoke and sacred song as an outpost of faith in the quickly transforming waterfront neighborhood.As he spoke to the hundreds of Boston-area residents who packed the pews yesterday afternoon, O’Malley recalled the disciples’ first Mass in the upper room of a Jerusalem home.