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ROS Navigation is built assuming a 2D model, the 3D interface here is not as it as written or intended so its not surprising that it doesn't work.

I don't think for this use-case is appropriate for the navigation stack, as it has a core assumption of 2D.

With that said, depending on how you have things configured, TF might know about the altitude you're flying at so your 2D LIDAR scan is looking over the marking at ground level. A 3D sensor in gazebo will certainly take this into account and try to avoid.