Been there, done that. Both with MoveIt and ros_control suffers/suffered (?) from this.
The referred lines were[ added by me](
https://github.com/ros/robot_model/pull/153) precisely with the purpose of changing those macros.
There were plenty of code using non-typedef-ed shared_ptr, the above two projects got through the trouble by adapting the macros, I have no knowledge of others.
[There is an effort](
https://github.com/ros/robot_model/issues/195) for finally brinding the urdf:: together.
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