By working on Pd's manual, I can see the current priority is to look first
in the directory containing the patch, then in the search paths. I still
want to maintain that structure. I just think that the order of the paths
should be different, first with "standard paths" (which includes 'extra')
then the user added paths.
I think you are right that the core "extra" externals should have priority. We've clearly de-emphasized users during everything into "extra" so, at this point, there shouldn't be much to break for people's setups.
That's my macOS perspective. I suppose the situation might be a little different for some Linux packages?