This article only scratches the surface of how messed up our health care system is. I'd be shocked if either hospital system was able to figure out how much money the writer's son actually cost the hospital... the organizations I've worked for take at least a year to calculate cost (if they ever successfully do it), making (as CWuestefeld said) many of their other calculations come largely from guesses. Sometimes that guess is as simple as "just multiply what Medicare pays by 3, and then charge the insurance company for that amount."
To compound this problem further, I've worked on federal grant applications that ask what the "cost of care" is. Since the hospital has no means of calculating this, I've been told to just sum the charges for each patient. As the writer experienced, the charges can often be a full order of magnitude greater than the cost. You can imagine how yucky this gets.
Someday I would like to walk in to a Best Buy, pick up a Playstation 3, and then inform the cashier that I will only be paying $20 for it. I wonder how well that would go over...