3 scenarios in the "real world", not 2.1. True bypass: effect is completely switched out of circuit (in other words, acts like it isn't there at all)
2. Buffered bypass: effect is turned on or off after an input/output buffer- can present a constant impedance input or output side. Also good for driving long runs (think Boss/Ibanez pedals etc )
3. Traditional mechanical bypass: input goes into the effect, as well as tapped, only the output is switched between the effect output or the input. The downside of this is that the input is ALWAYS affected by the input impedance of the effect. Most of the classic effects like fuzz face, crybaby wah, all of,the old click switch MXR/DOD effects of the 70s and 80s work like this. Also what I suspect that the Helix is emulating when modeling specific effects.