My experience of group drift diving is as the divers go out of air as the dive progress, the DM will send them up, I've seen that happen countless times, sometimes a single diver even and not a buddy pair. This could have been a diver still rising and a boat going by not seeing the diver coming from below. IMHO this is why every diver from OW level should have a SMB and know how to deploy. If you're a buddy pair or solo and rising to the surface no one will know, the marker bouy is dragged by the DM, who is now a long distance away from you after your safety stop, you are unmarked and unknown, especially where multiple operators are in the area, they only focus on their DM's marker.
While it is possible something very unusual happened, what you are describing is not how things are done in South Florida and on that boat. (Yes, I have done drift diving off of that boat.)
Divers are generally put in the water in small groups, usually just buddy teams. With most operators, there is no DM in the water. (This operator never put a DM in the water when I used them, but it has been about 3 years since I have used them, and it is possible they changed.) The only one I know in that area that puts a DM in the water does so for the benefit of any divers who may want one, and usually it is only a couple people at most. The dive teams all pull a dive flag that floats on the surface, and the boat follows along as they drift staying a safe distance away while still maintaining contact. As teams finish their dives, they typically ascend together, reeling in the line from the dive flag as they do. They reach the surface together next to the flag, and the boat comes to pick them up. In the unusual event that a diver in a group wants to ascend early, the diver follows the dive flag line to the surface and comes up next to the flag.
The only time a diver should be surfacing away from the flag would be a mistake, such as getting separated from the diver holding the flag. (Groups are typically warned that the only diver who is never lost in the group is the one with the flag.) If a diver does get separated, then a DSMB is very much a good idea. If a diver does surface after such a separation without a DSMB, then that diver will not be far from a flag[ in fact, the diver will usually be within a cluster of flags which should keep other boats away.
I was separated from the flag once last year, but that was a very unusual occurrence. Another boat had a single diver hunting, and he had hooked the line on the reef while he went off hunting, getting pretty far away from his flag. (That is illegal, BTW.) He surfaced in our cluster, and our boat notified his boat. They picked him up and then returned to retrieve the flag he had hooked on the reef. Feeling the expected resistance of the reef when they tried to lift it, the boat went to full power to break it loose. They probably wondered why my boat was blowing its horn as they did. Anyway, eventually they realized that it was not their flag they were lifting, but mine. When I realized I was about to undertake an unscheduled water skiing adventure, I let go of the flag and deployed a DSMB.