A 1K on an M fare should have trumped a CPU in any event.
But, the fact is that once you board, you have lost your place on the UG list unless you have made specific arrangements w. the GA and the GA has specifically agreed to come find you if you make it.
What you saw here isn't likely shennanigans, but rather exactly why it is a bad idea -- other than for the pax who misses the UG -- to disrupt the boarding process for UG's. Messing around finding people on a list as the clock ticks down is exactly what delays flights.
This is one where, had OP waited at the gate because F had not boarded full, he would have been standing there when the seat came open (and presumably #1 had boarded or not and lost his slot).