The reason the ATM has a limit is because it's eventually consistent. It's possible you just went to another ATM and drained your account, but that hasn't reached the main office yet.
They are limiting their risk by allowing you to defraud them of up to $500 (or whatever your limit is).
It is true in some sense that the banking system is eventually consistent, because commands can be issued asynchronously. For example, you can issue a check, and expect it to be drawn in the future. However, that does not necessarily apply to the ledger itself, and given what I understand about banking technology, I'm somewhat surprised if it is truly as you describe.
If it is indeed a conjecture of yours, I urge you to make it more clear in your comments when you are speculating and when you are speaking with authority.
It's true there are other reasons for the limits, such as the ones you listed, but if you are with say Bank of America, your limit and my limit can be different. The more credit history you've built up with the bank, the higher the limit will be. This is mostly because they trust you more and therefore consider the risk for defrauding smaller.
99.999% of the time? It's impossible to guarantee that 100% of the time.
http://www.nytimes.com/2013/05/10/nyregion/eight-charged-in-...
If what you are saying is true it would be possible to go overdrawn at an ATM. This (again AFAIK) doesn’t happen as there is a call to check your balance.
It is most definitely possible, it just rarely happens because the network doesn't fail often.
See here for more sources: https://www.google.com/search?q=eventual+consistency+atm
See also this article where hackers stole $45 million from ATMs:
http://www.nytimes.com/2013/05/10/nyregion/eight-charged-in-...