Providing you have connected both the rx and tx lines of the serial comms, you can simply add a chip reset wire and use avrdude with rpi-avrdude as described in the rfm2pi wikis. I used to do it all the time at one stage.
Are you saying you are powering the zero from the ac:ac adapter via the emontx? I’ve never tried that as I expected the zero to significantly deform the voltage waveform at the very least.
IMO in all aspects the zero is superior to the esp method and factoring in the price and the sdcard, it’s still a winner. Even more so when hosting emoncms on it too (i know you prefer to seperate them though) for an all in one solution like an emonpi with 4cts for considerably less money.