It also leaves you a one-block-long tunnel for a train, and another for a road, for years until you get the blocks around it done - probably for decades until you get a system that goes anywhere.
Sure, but you have to start somewhere. Why waste money digging up the same street over and over, as most cities do? It seems more efficient to do it once and be done for a long time thereafter.
At least you're getting something back. When the channel between Dover and Calais was bored, one of the boring machines was simply left underground, because it would have been to expensive to retrieve it.
Also, you could easily imagine doing this to a part of the block that's up on a hill - Seattle and SF have a lot of areas like this. It would make piping existing traffic into and out of those transit sections easy.