Bypass of In1/Out1 works fine when running stereo, but only for In1/Out1, while In2/Out2 will always be processed. You could use "software bypass" for In2/Out2 with a direct connection, or switched connection via one of the switch utility plugins, but the signal will go thru A2D and D2A conversion unlike In1/Out1 which when bypassed is truely passed as analog.
That design decision was made to avoid another relay, two transistors, board space and two additional GPIO's, when the main usecase for true bypass is mono guitar signals.