Content entries should not intersect

We have an existing project structure that basically works like this:
/project_folder (no
    /extra (no
      [additional libraries]

Both /project folder and /project_folder/content/extra should be in the Python path (sys.path) for proper functioning.
When I create the project it makes /project_folder a content root. But if I try to add extra, it gives me an error ending "Content entries should not intersect." and does not allow it.

Is there a work-around for this? I think the warning is misguided, as /extra is not a python package...
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Co-worker pointed out that I can manipulate the Python path directly for the interpreter. This works but since the 'extra' folder has a different absolute location per project, it does not scale at all.

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