Plan "B" is always in the wings. The lower tracks out by and including the current FEC are at the tunnel mouth (one they created when they cut into it) add platform and one or two more tracks South of FEC and there is room for Amtrak now.
Then stub the upper level tracks, Skyway etc. at the viaduct. They'd still have room for commuter rail, light rail, Skyway, or for shorter Amtrak Trains or "Sections" of trains and the tunnels COULD BE USED again.