Please help with RTC and interrupts

Yes, that's right. If the logic power fails, then D13 will drift to ground, or at least one diode drop above ground, and the converter will turn on. The datasheet says if pin 5 is open, the regulator will be on. So to make it shut down when logic power is off, you would need a pullup resistor on pin 5, then an intermediate NPN transistor (or you could use the mosfet for that). So to turn on the regulator you would bring D13 high, which would turn on the NPN, which would ground pin 5. If logic power shuts down, the NPN would be off, and the pullup resistor on pin 5 would take over. But of course this uses additional current through the pullup resistor and the NPN base when the regulator is on. So if it's not really a problem, i wouldn't bother with all that.

But for future reference, notice that the Enable pins on the linear regulators are active high.