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My question to this would be:
Why would you want to use a 40cm puppet, when it is easier and more stable to capture a human doing the same motions, then apply it to your puppet size in Motion Builder?
This isn't a real-time system, so you can't puppet to appear in live action video.
As you know the Kinects are based on depth perception and a point cloud, so anything in the point cloud will become trackable, (i.e. the "rods"), and may cause severe issues in the tracking process, thinking that part of the depth is a leg, arm, puppeteer, etc, but you could minimize this with a separation curtain with the puppeteers behind it and closer to the puppet, you just would have to test it out.
There are fans of the Kinect sensors, I am not one of them, but maybe some can offer more experience as to the tracking ability for the process you want to perform.
Four, or more PS Eyes would give a cleaner tracking result in my opinion, as the "rods" wouldn't get detected as long as were a completely different color than the puppets clothing, bones if a skeleton as shown, white is a good color to use for PS Eyes not to detect, but also depends on the characters appearance and the background colors present.
This is most likely a "try it and see" for the process you are attempting with Kinect sensors.
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