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It depends on how you define the visual and collision elements. For example, you have a base_link which is in the center of the robot. If the origin of the robot mesh is not defined at the center, you will see that the mesh does not match for the actual definition.

Example: let us say that you have a cylinder-shaped robot, and base_link origin is in the center of the bottom face. If your cylinder mesh is centered in the center of mass (for instance) of the cylinder, you would have to move the origin of the visualization/collision in the Z direction by height/2.