That unfortunately is an American centric problem, it’s particularly bad in NY but other parts of the country aren’t immune to it either. There’s a lot written about that elsewhere.

My point in this instance is that even at the inflated construction costs you could still accomplish a lot more with better planning and linking these systems up. A tunnel and new stops in manhatten connecting them is going to accomplish a lot more for the same price as capping a huge rail yard. Building new tunnels that terminate three separate systems in different locations. And building a new Penn station.