How should I use the humidifier’s bypass option

The calibration instructions (on page 2) require a specific set of conditions which may be challenging to adequately create and control—especially if anyone else is in the building.

I would begin by making sure the mechanism operates smoothly and freely. Also be sure that the device is installed so that the pipe is exactly parallel (or vertical) to the floor and the wire penetration is centered so that its movement isn't affected by going through odd angles with respect to gravity. Almost certainly the damper being stuck is caused by either mechanical friction or disorientation to gravity.

After that, repositioning the weight for proper operation should be easy.

I've thought the same but think you want a fairly big fan. You are fighting to keep the ultrasonic droplets from condensing on surfaces. You need to supply enough air flow for them to evaporate and not condense. Position the output somewhere where a dribble caused by condensation won't wreck a motor or electronics