If there's no pullup resistor on that line on the module, then you can configure the GPIO as INPUT_PULLUP. And then you can power down the module's Vcc pin, but the alarm will still work. But if there's a pullup on the module tied to the module's Vcc, then you have to keep Vcc high while waiting for the alarm to trigger. The DS3231 uses about 50 times more power running on Vcc than it does running on the coin battery, so you want to power it down when you can. The coin cell will still last a long time.
It just seems they could have connected pin 4 to something - anything that might be useful - rather than leaving it NC. And the most useful thing would be the alarm pin.