My Wife was in NYC heading to DC and said that she boarded her Acela to DC from the lower level without any issue, nobody was present to stop her or the other pax who boarded from the Lower Level.
I have done it twice and neither time was an AMTRAK employee on the Lower Level doing any sort of checking. In fact once I ran into an AMTRAK Police Officer in the elevator and he asked where I was going, I replied Washington and he wished me a safe trip and said I was smart to avoid the scrum on the main level.