Not so sure I understand what you're getting at here, and on top of that I believe you're confusing spillover with bypass. Spillover is for when you're changing from one preset to another, it allows tails instead of an immediate cutoff. Spillover has no bearing on bypass states.
It seems to me like your pedal is operating as expected. What you are experiencing is the bypass setting you're using: DSP, Relay, or DSP+FX. The state of the pedal and how it's running the algorithm with input/output as a function of the bypass/active switch is directly related to THESE settings, NOT spillover. Each is explained in-depth in the manual.
It sounds to me like you want to switch to relay bypass.
