Just to clarify, there are already 3 floors in Term E, and the existing lounges are on the 2nd level.
A few years ago, they redid E. Until then, the only entrance was the ground floor, which was (and still is) used for arrivals, including customs. To get to the 3rd-floor departure level, you took one escalator to the second level, then a second, adjacent escalator to the departures. To get to the lounges, you'd take the first elevator to Level 2. There was also a balcony on that 2nd level, from which you could look down to the check-in areas.
When they refurbed E, they added roadway access to the 3rd/departure level, and they removed the sets of escalators that stopped at the 2nd floor. They also completely enclosed the 2nd floor area. The only way for the public to get to the 2nd level for lounges is to take the elevator or stairs down from level 3 to level 2. None of the lounges have windows AFAIK, so it does indeed give the feeling of being in a basement -- but you're really just in a limbo area between arrivals and departures.
All that said, hurray for adding lounge space. I think I've been in every one of the BOS lounges except the Virgin Clubhouse, and there's not 1 that gets a better grade than C-.