Howdy, thanks for trying PhotoStructure!
This is actually expected behavior. Here’s the details for what “automatic organization” does.
(specifically, all four images are copied because they all have unique SHAs).
Apologies! This is a bug: all four (or eight, after it copies stuff into your library!) should be aggregated into a single asset.
If you could DM or email me example images that aren’t being de-duped properly, I can see what’s going on and update the deduping heuristics.
FWIW, these deduping heuristics are under continuous improvement: just yesterday I added support for Google Photos that had metadata deletions: