This is absolutely true. But the question is
why are they stuck at that rudimentary level?
My wife is at the center of this. She recently left a job as "Director of Budget and Reimbursement", and now works as "Directory for Regulatory Affairs" for a healthcare financial consultancy. So she's been the one directly responsible for the way the hospital accounts for its costs (or fails to do so).
The primary problem, at least from her perspective, is that they're effectively forced to do it this way. Medicare, and Medicaid which largely rides on many of -care's definitional coattails, is a monopsony player in the market. When you hear people claim that Medicare is more efficient than conventional commercial insurance, that's significantly because they offload much of their administrative burden onto the healthcare providers. Every hospital has a department of several FTEs whose job it is to track a defined set of metrics, including various cost parameters, patient demographics, etc., and report them to the government (the so-called "Medicare Cost Report" that my wife and her department spent a month or so on every year). That is, getting paid by the source of the largest part of the hospital's revenue entails tracking and reporting the way Medicare wants you to do it.
So that right there forces hospitals into watching their costs according to a scheme effectively mandated by the government. Thus, they're not tracking the data in a way that would give relevant cost accounting data in the way you expect it.
There's your proximate cause. But it still begs the question, "why don't they also track costs in a rational fashion, actually reflecting reality?". Part of the answer is that their margins are so low that they simply can't afford a second set of accountants and the procedural overhead that it would require.
That's not a wholly satisfying answer, because hospitals are the only industry I'm aware of that still makes extensive use of secretaries. You'd think that if they need to be so conscious of costs, they'd be looking at the kind of personnel expenses that most of private industry has figured out how to streamline. Conversation with my wife hasn't yielded any insight beyond that.