My best guess as to why we got the " Error: G1/G2/G3: Intermediate position outside machine boundaries" error is because, in principle, each move should be terminated with triggering and endstop. A free-spinning shaft that would violate that principle.
Good to know how this hardware issue can manifest. I'll update the instructions to make sure folks double-check that their setscrews are threadlocked and biting down on the flat part of the shaft so this hopefully doesn't bite someone in the future!