To duplicate the features of ATXRaspi and monitor the battery level and make decisions, I published a sample sketch here. Use a simple Moteino (no transceiver needed) to control MightyBoost and emulate the behavior of ATXRaspi. If you want to get fancy and send control messages and get battery level over wireless you will need to add a transceiver to your Moteino.
When pairing with Moteino: the BootOK signal coming from a RaspberryPi will be around 1.7V even after the Pi shuts off. It’s not entirely clear if this was always the case or it started happening with recent distributions of Rasbpian. This causes the BootOK signal to read as HIGH on the 3.3V running Moteino. This is not an issue on ATXRaspi since that board runs at 5V and 1.7V will read as LOW. To fix this issue, the BootOK signal in MightyBoost R2 has been moved to A0 (D14) and the sketch will read A0 (D14) for the BootOK signal. If you have a MightyBoost R1 please see the guide for differences.