Any such company that doesn't do a simple head count should be put out of business. There is no excuse for not doing one.
To extend your point a bit: simply telling divers to “stay in a designated area” does not allow for the fact that it is difficult to swim against a current of as little as 2 knots. You could literally find yourself in such a situation by crossing onto the otherside of a reef head.
Then, following another dive rule (if separated for more than a few minutes, surface) you could be hidden in the surface chop a mile from the boat. Surface currents do the rest.
It’s the dive operator’s ultimate responsibility to provide adequate dive supervision & account for the divers at the end of the dive.