If/when they get another anchor tenant, that will be the main public entrance for that tenant. But it's currently used for the temporary loading dock, so that's why it looks the way it does at the moment. Since the whole base is thick, blast-proof concrete, they had to use one of the few openings, and that was it.
I assume the temporary loading dock is still there for essentially the reason weidncol said: The temporary PATH entrance blocked a connection between the underground vehicle areas and the permanent 1WTC loading docks deep underground. And of course the VSC isn't even finished yet, so those underground vehicle areas aren't very useful yet anyway.