Everybody who has come out has recommended a bypass, which is completely wrong, as you and others have pointed out.
I don't have the vacation time (or the money) to keep calling out endless technicians who don't know what they're talking about. How can I find someone who actually knows what they're doing? What questions do I ask on the phone? How do I talk to right person? How do I make sure they send someone qualified to assess and address the problem?
(The guy who installed it apparently knew enough not to install a bypass, but he was a total flake about showing up, repeatedly forgetting appointments.)
I'm guessing from the resounding silence that this is a tough question when you don't already know somebody in the area.
What would you (knowing what you know as a pro) do if you had to find a pro you could trust?
A bypass humidifier connected to the cold water line will actually help to keep your furnace from over heating when only one zone is calling, and the humidifier is on.
Plus when the humidifier is mounted on the return and the bypass is connected to the supply, its safer for the furnace if the humidifier ever has an over flow problem.