That's an interesting read, but quite off topic here: we don't have cables degrading our signals in Helix, and some fuzz pedals don't work correctly if preceded by a buffer or by an high impedance device. So a 'true bypass like' implementation is the only way to have the realistic input load on fuzz emulations without the dull sound of a low impedance setting when the fuzz is bypassed.
There's no "high impedance device". A buffer has a high input impedance, but a low impedance output signal. The high impedance makes so the signal isn't messed with when it comes in, out goes a low impedance "SIGNAL", a low impedance signal isn't as easily affected by long running cables.
I have been holding off on saying anything.... as I don't think referencing "impedance" is the issue.
However... especially in a digital world, the video is very clearly unexpected behavior. This could be a real issue with complex snapshots and likely is.
Bottom line... I agree... If you have a preset setup... with an amp, and another preset setup with an effect and an amp... if the effect is bypassed, both presets should sound the same. That's simple logic.
An option for Bypass (True or Buffered) on the appropriate pedals might be a good solution, as well as many others suggested. I find the Line 6 folks are pretty smart, so at this point I assume they see the problem (if they see it as a problem) and will address it in some clever way none of us thought of.
It's not about bypass. Think the input impedance is the front end of every effect, but this is a crucial part that can't be digitally recreated as of now, it needs to be analog, that's why devices like Helix, Eleven Rack and Axe-fx II has an analog version of it, but controlled digitally so it can change value.
What's the problem with Helix? Other devices set the input impedance to match the fist active effect. In the video example, what effectively is happening is that when I have the Fuzz Face first, it does't matter what goes after it, Helix will stick to the same front end. When I turn it off, what's happening is that I have the amp with the front end of a Fuzz Face, that's why it sounds wrong. It's like putting a pig nose on a fish. In the analog world I could build the fish with the pig nose while still making it true bypass. Do you get that? I's "NOT" about bypass.