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I can write a more extensive answer later, but for now: no, there is no support for festooning joint limits anywhere in ROS. Not in URDF, SDF or any consumers of those formats (joint_state_publisher, robot_state_publisher or Gazebo). MoveIt! does also not support this.

The big assumption in almost everything that deals with robot kinematics and geometry is that the structure is defined once, loaded at application startup and does not change.

Perhaps if you can describe your robot better (diagram or picture), we can suggest alternatives / work-arounds.