This distinction is important if you have a load balancer in front of nginx. The LB will wait until timeout for a response, occupying a bit of stateful memory and probably causing an error which is indistinguishable from "backend application server is offline".
On a well configured site the LB timeouts should be short enough anyway.
But it is a risk, especially on classic DOS attacks.
The other problem, if you are behind an LB, is that the client (DoS attacker) will get a 503 from the LB after timeout. So, no gain even if your timeouts are reasonable.
It'd be great if you could return a custom response from nginx that would tell the LB to drop the request -- or you could move the exploit-detection logic to the LB instead of nginx, and the LB could do its own 444 equivalent.