You could write the files to the pi system, and call a bash command as sudo to copy them to /boot.

I installed bridgeutils on the pi3b+ and added eth0 and usb0 to the bridge, the pi 0 boots and it's usb0 is also bridged with the eth0 & usb0 on the host pi3B+. so I can run mjpg streamer on the pi 0 and access it from my home network. I can directly ssh into the pi 0 at the USB interface. Trying no...