How did you install emoncms? Assuming a Pi 2/3 (not sure about the 4, bluetooth and one of the serial ports are shared. I think the standard install of emoncms effictively turns off the bluetooth.
There is some info in this post Multiple problems w. EmonTx and RFM69Pi
@TrystanLea , perhaps configuring the serial port should be an actual option in the install scripts rather than a decision based on the RPi environment flag.