The steel beyond Water Street appears to be weathered, so it won't get painted at any point in time. I'm guessing the beginning of the new viaduct (at Lechmere) had some type of requirement by the MBTA to match the look/feel of the existing viaduct.
I think that would be messy.. the commuter rail and light rail have different geometrical requirements for vertical and horizontal curvature - so I think it's better to keep the inbound and outbound tracks for each of them grouped together.
That area near Lowell Street bridge is the end of Magoun Square station. I believe they will need their own structure for the entrance to that end of the station, other than that the majority of that existing retaining wall should remain as is.
Correct. The retaining wall on the right is just pushed in toward the tracks because there is an existing retaining wall behind it that is deteriorating but too close to homes to replace in kind.