Traffic today is very heavily weighted in the Cove direction, so NEC trains are the ones that cross the most switches to fan out across the middle platforms. That wouldn’t be a problem if these were all 100% T trains running push-pull and those switches could just stay set in the Cove...
For projects like this (as well as proposed floodgates that could provide near-impenetrable protection for New Orleans), the pricetags always sound completely reasonable to me. For a project like this — which would protect hundreds of thousands of people, safeguard billions of dollars in assets ...