EDIT: Just realized you're talking about the Vehicle Cloning system.
Perhaps it is one of the other logics that's interfering with it. Try it without FactoryPlant lines, and then again without WeaponsFactory. I'll have to test this myself. QUICK_EDIT
Removing WeaponsFactory=yes will make the units appear outside of the building, rather than walk out like from a War Factory. Naval yards don't have it, and they still can use waypoints.
Infantry cloning facilities allow waypoints with just Cloning=yes, so it's most likely just a limiation of CloningFacility=yes. Or a recent bug. QUICK_EDIT
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