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It looks to me like the markers are generated inside planning_components_visualizer.cpp in the move_arm package:

Joint Markers:
Look in createSelectableJointMarker. In particular, the scale is set using the maxDimension parameter. For joints with mesh geometry, this is calculated based on the mesh vertex location with some odd assumptions. For other joints (with cylinder/box geometry), the scale is set to a fixed value. It looks like all markers should have a scale in the range of 0.15 to 0.5.

End-Effector Marker:
It's a little less clear how the end-effector marker is generated. I believe this is also created in the same file. It looks like it's related to the PlanningComponentsVisualizer::EndEffectorControl type and the makeInteractive6DOFMarker topic. Perhaps this marker is always created with a fixed size of 0.225.

Hope this helps!