"But this isn’t about the money. It’s mind-boggling how many people must have failed to do their jobs properly for this to be able to happen. Furthermore, surely numerous FAA regulations must been violated, e.g., surely flight crews are required to positively verify that the number of passengers on the manifest matches the number of passengers on the plane."

That's why we count heads before push. To change the count on the paperwork if necessary.

And I'll bet it IS about the money.