Apparently, this is an expected behavior.
From Neural Support:
"This is currently expected behavior. When using Pre Roll with Looper X, the metronome will continue during the recording phase so the performer can keep time accurately while laying down the loop. The metronome is not included in the recorded loop playback itself.
We do understand how this could be problematic in a live setting when the metronome is routed through the main outputs, and we appreciate the feedback."
I have started a feature requisition for the option to turn this off.