I've seen a lot of 3PDT True Bypass wiring methods that ground the Input of the effect when bypassed, but not the output. Is there any reason not to do this? (Other than the obvious hassle of adding a second jumper.)
No particular reason why not. I guess the question I have is what is being achieved. Don't get me wrong - I like using belts and suspenders in parallel backup arrangements.
But if the input is grounded, the output is quiet unless the thing oscillates all by itself and can broadcast its output across the switch gap that's open from the output to the signal lines. And if the output is grounded, internal oscillation could broadcast through the ether. Maybe a poor wiring job makes the power ground and signal ground share a line and current wobbling on the shared ground could get into the signal line. Grounding the input is probably a better way to keep the circuit quiet.
I've even seen setsups that ground somewhere in the middle of the effect circuit.
Given that hard-contact true bypass will always have some amount of clicking depending on how unlucky you are in where in the signal cycle the contacts close, I prefer one of the several other ways to bypass. And the Millenium C will let you mute as many places in the circuit you like.
Anyway, if it seems good to you, no reason why not.