Through the normally-closed reed switch. Seems like the leakage would outweigh the power saving of this design.
You just have to momentarily GND the mosfet gate with a pushbutton to turn it on manually. And an open collector gpio to keep it ON the rest of the time.
Could it be done without a switch, so that the microcontroller starts as soon as the device is powered?
In my circuit, the magnetic switch is closed when the magnet is NOT present, and that happens when the door is opened. Closing the door brings the magnet next to the switch, which opens the switch. So no current is flowing while the mailbox door is closed, which is almost all the time. Then after the mosfet turns on, it supplies power to the microcontroller which boots up. The first thing it does is assert that GPIO pin as a high output, which turns on the NPN, thus providing a second path to ground for the mosfet gate. So the controller latches the power on so it stays on after the door is closed. Then ultimately it shuts off its own power by bringing the GPIO low.
In your case, the switch would be replaced by the /INT output of the RTC module. That's an open-drain output, which can only pull the pin low when it's active. So it will draw no current until it's time to power up. You might not need the NPN transistor at all if the module can keep /INT low until you tell it otherwise. Then when you're ready to power down, you send the appropriate command to the module over I2C.
One potential problem is if the /INT pin has protection diodes that would come into play if the main battery voltage is high enough. There shouldn't be any on an open-drain output, but I haven't checked the datasheets.
The ony remaining issue is whether the microcontoller can assert the GPIO high before the /INT turns off. If that's a problem, adding a capacitor should solve it.
The whole idea here is that even when it is running, the RTC module uses far less current than the main circuit uses when sleeping. And if it's running on its own coin cell, no current would flow from the main battery when the main circuit is off. So instead of putting the microcontroller to sleep, which still leaves the regulator running and possibly other stuff, you just shut down the main battery power altogether, and let the RTC power everything up again at the right time.