How to control power from 12V battery to RPi with a microcontroller
Since the crux of the question is how U1 can control power to the RPZ, and U1 has its own power source, the answer is simple - use one of the free pins on U1 to control U2.  U2 is a LM2596, which has a control pin (pin 5 on the TI datasheet), so:


Wire up pin 5 of U2 to, say, PIN4 on U1 (if PIN4 is meant for that function).
Connect the grounds of the two circuits for common potential.
Program U1 PIN4 to control the power regulator as desired.