If we're looking for a way to build HSR or at the least, move away from the slow and seismically obsolete Steel Bridge, would it theoretically be possible to bury the tracks at Union Station underground via cut and cover? Then continue under the Willamette and through the central eastside? We could cut and cover with minimal opposition to the disruption down 3rd Ave and pop up again south of division. This alignment would allow expansion of the capacity limited union station over the tracks, separate passenger ROW through the city center from freight and also make pedestrian/bike connections to Naito easier by removing the barrier currently presented by the tracks.
Problems? If all surface level tracks are removed then the small amount of freight traffic that runs across the steel bridge currently would need to be rerouted somehow, and anything underground would have to contend with a MAX tunnel through the area should that ever get built.