If the signal loss is so bad, then instead of a true bypass they must be converting analog-to-digital, then have a split for the 'clean' signal and the control signal for the synth module, and then a digital-to-analog conversion for the guitar output. Each conversion will take a bite out of the signal.
You do need a reasonably flat signal for controlling the synth modules (for instance your sustained notes would drop off early) so that's probably why the digital signal is lifeless.