Well the behaviour isn't so clear, and to be honest I have never took care of it so didn't noticed the working.
It sould simply add what you put in default folders to any new project, not to all projects you open. And this is consistent because if in a project you removed some folders it would be uncorrect that the IDE added them again each time you open it.
I.e. when you freshly create a project the IDE insert the folders for include files and libraries, then, if you have any, appends folders from default settings. No modifications are applied to the project on any opening of existent projects.
So I don't think this is a bug at all.
i catch up your viewpoint and do not surprised at all. It comes from your personal practice... Let us consider the situation. You are novice in some technology (MPI for the instance).. good and most relayble way to master it (at whole) through many exisices (small ones). With usage of the IDE (at its current state) you front before the necessity of setting up folders and lib files for every project. So I (as senior lecturer) check that feature (that is not important in your practice) before long. For It is up for me to recommend the IDE as main instrument for my students or do not ... and I bear all responsibility for the choice.
But , nevertheless,there is someone at the forum who says :WHAT ARE 2 other choices of folders combo ( Includes, Library) FOR?
If one looks at the embedded reference one sees:
"....What you change here are the global settings for the environment variables PATH, LIB, and INCLUDE. Changes here will affect the entire IDE: project build commands, tool commands, and so on. Projects will use the global settings by default, but can have local settings for the LIB and INCLUDE variables; see Project options, Folder tab...." - declared functionality that i talk you about.. But It does not do what it is proposed to... If it is not the bug... let us over with the discussion.