Because banks have kept antiquated policies that go back to a time before computers for no other reason other than that it makes them a lot of money. At some point in history your bank account ledger would have been kept hand written on paper that folded out to what they called (get this) a spreadsheet. Each ledger would have been kept at the single branch where the account was opened. Another branch across town would have no idea what your balance was so they would have to accept charges before physically mailing it to your local branch for processing. If the payment didn't clear but the bank had already paid on your behalf then it made sense to charge a fine.
These days literally the only reason for a bank to let an account overdraw is because it makes them a lot of money. They don't care that they are getting rich off of the poorest among us. In my eyes they're no better than sleazy payday loan centers.