Thank you for the additional clue to find out how to address the issue —  in reading under the System Menu Tree, p 32 of the TF manual, the capabilities for controlling input and DSP signals you describe are presented.

For clarities sake, however, the issue is caused by discharge at the pedal's output (to the Ethos) during startup (of the TF) when no input signal is fed into the TF — ie., not by input where bypass selection is directed to input and DSP signals reaching the output.

If I understand your suggestion properly.