Unfortunately I don’t really have a good answer for this, but your posts did help me understand pijul a little bit more. I think you ran into a similar thing that I ran into when I playing around with pijul and posted this question: Is there a way of telling if changes, saved in text files, will conflict? (although the question I ended up asking was different).
Basically, you sometimes run into a situation where you don’t actually have a conflict, but pijul thinks that you do. You, the programmer, know that the resulting file is exactly the same, but pijul thinks that something needs to be reconciled, even though the diffs produce the same result.
Your comment about pijul using “patches identified by hashes” instead of just diffs is good to know.