You aren't missing anything, the connections are easier compared to the older Lionel TMCC equipment. Plug the Legacy Command Base into an 120Vac outlet with a third prong, then a wire from the U terminal to the outside rails.
Then hook an AC transformer to the Molex style connection (the 180W brick makes it sooo easy), then the other two binding posts to the track, with the one labelled U going to the outer rails. And obviously plug that transformer into an 120VAC outlet.
That's it, no more connections. The new Legacy PowerMaster listens into the 450 or 455 kHz on the track and on the U terminal; so that signal could be coming from the Legacy Command Base, it could come from an old Command Base, or it could be whatever that new Legacy remote base that I am not familar with.