everyone was accomodated - potentially everyone had a seat. Schedules have to be kept - planes have to leave at certain times to get somewhere else at a certain time. It's definately a balancing act for the (one) GA to be both on the plane to give upgrades to someone that went ahead and boarded with the elite pre-board instead of waiting for a seat to maybe be empty and also wait and give that last paid F customer his seat.
The most recent time I saw this happen was when I was involved with a connection at DTW because it was much tighter than it was supposed to be.
I flew in on a Saab out of FNT and wound up with less than twenty minutes to get off the plane, get from puddle jumper land, through the tunnel on the tram and to the south end of the A Concourse. All I told the GA just before I got on the plane was Mesabe has made my day interesting (the connection was supposed to be one hour plus).
There was an open seat in FC, they were about to close the door and I was happy to be on the right side of the door and wasn't very concerned about where I sat.
BTW, compared to the Saab, a coach seat on an air bus felt very comfortable !
Bob H