I FOUND IT! Sure enough, on the top side of the flight controller PCB is the PPM connector I had theorized about. Poked the board with my multimeter to figure out the pinnout (shown below). Just placed an order for a Flysky micro PPM receiver. Now waiting for my order from Banggood to show up...

EDIT: Just like on the real 3DR Pixhawk, the PPM port also accepts S-BUS and, with a firmware update, i-bus (what I'll be using).