Avrdude doesn’t have the ability to control the reset via a gpio pin itself. There is a utility called avrdude-rpi that triggers any preset gpio pin for reset purposes.
OEM have a version that is installed to all emonSD images so it works fairly automatically once installed. There are instructions on how to install in the repo too, I hope they are still up to date, they were written years ago.
Not necessarily, if you only need to do it once then yes, but if you want the ability to upload new FW without fetching the USB programmer, then once you install this utility it is no different to USB, just a different address. The gpio pin is hardcoded in the utility to gpio4 (pin7) for the rfm2pi and emonpi, but you can use any pin. Obviously you will need both the TX and RX lines for upload if you don’t already have them connected for normal running.