The 4,6,7,171,448, and 449 busses are non-Silverline busses servicing the Seaport.
As for a walkway protected from the weather? I don't know. I hope not. Weather and light are a part of the equation in experiencing any part of the city. I can experience a hallway lots of places.
The idea brings to mind Copley and the triangle between the Mall, Library, and Pru. It is a place to get through, not a place to experience. And at street level is nothing I would consider vibrant.
The last thing I would like is for the Waterfront to be handed over in a similar manner. Considering the wonderful Harborwalk, this would seem counter intuitive. Although an alternative, it could easily be leverage for apathy in favor of less considerate development.