You initial reading was correct. I don’t want photostructure to delete anything outside of the “plus” library. In fact, I mount the scanned folders read-only just to be extra sure.
I’d like the “plus” library to have only the “best” version of every asset. Basically a “physical” de-duping and not just a logical de-duping. Of course, all of the duplicates in the source paths would still be there should I disagree with a decision that photostructure made, so there really is no data loss should photostructure do something stupid.
So your ideas sound ok to me.
An additional idea that just came to mind just now - maybe worth exploring: could one specify (either through UI or configurations) a source folder that should always take precedence? Or even a ranking/weight for each folder? Thinking about my situation: there is one source path that I actively manage (edit metadata, post new pictures) while the other paths are more historical. You can see in my screenshot 3 paths: “ApplePhotos”, “GoogleTakeout” and “oldNas”. Really the ApplePhotos is the one copy that should always win in my book, with “oldNas” coming second and “GoogleTakeout” last. So the paths could be given extra consideration in the heuristic.