I called MP and got an answer. Not everybody in my party has elite status, so when I look at the seat map through the existing reservation, E+ is blocked out - even though our seats are in E+ because two of us are Premier Executive (and the other two were "pulled up" to E+ when I booked over the phone). Note that dot bomb does not recognize the "pull up" practice, so it will not show availability of other E+ seats.

Meanwhile, when I was checking seating through a revenue booking, I was doing that as one person who has access to E+, so I could see all those empty seats.

Case closed (although there still were a few seats discrepancy even after accounting for all this).