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I think that overlaying is the simplest way if you are developing ROS programs, you will just need to use catkin_make_isolated because of OMPL packaging.

And have no fear, you have complete control over it. catkin will find the underlay at compilation time only if you have sourced from its devel/setup.bash or install/setup.bash (devel_isolated and install_isolated for catkin_make_isolated) in your CURRENT shell.