At the moment the LED is switched off when bypass mode is engaged, or when the pedal starts up in bypass mode.
If you consequently press the button, the LED will light up again.
I agree that this can be confusing.
Ideally I think the LED should respond regardless of bypass state, but switch off after e.g. 1 sec if in bypass mode. That is a little bit tricky to achieve in the firmware without adding a conditional in the audio block process loop, which is why it's not been done yet.
I think that having it permanently off in bypass mode is not a good solution since the pedal would appear non-responsive.