The only way to detect would be to test the different baud rates.
However, updating the RFM69Pi firmware is unlikely to be needed, there has been any changes to the RFM60Pi firmware since 2016: Release V1.3.0 · openenergymonitor/RFM2Pi · GitHub. Therefore, as an emonBase user is doesn’t really matter if you run emonPi update instead of emonBase update since there is no new FW updates.
I agree, it would be good to make the microcontroller FW update a separate process from the emoncms update