There is no doubt that this will provide greater flexibility, but a curious mind remains curious (and unsatisfied) forever. The cost of this work is definitely in the millions and is certainly keeping a few crews busy for quite a few months. With ESA, the Hartford Line and the Penn Track renewal going on at the same time, one would think that if a project (such as this Empire connector switches) is being concurrently worked on, then the pay off of such project would be somewhat more tangible than a vague "greater flexibility".
One must wonder whether making the Empire trains arrive and depart on tracks 1 or 2 (as long as they do not need servicing at Sunnyside, or maybe move all the servicing to Albany) is not flexible enough. It eliminates intersecting moves between the Empire trains and the NJT trains on the low-numbered tracks. It eliminates a few moves through the East River tunnels too. You obviously cannot do that once the new tunnel is built, but till then what flexibility is this work really buying Amtrak that it is worth spending the money now as opposed to the time when new tunnels are actually being built?
I know that this is just forum on the net and I do not expect authoritative answers, it is that I just cannot make sense of this and hope that someone else can.