E.g. if you merge two branches with the same patches but in different order, but the file contents are the same at the end, git will need to you to manually address the merges for each patch. In a patch based system, there is no conflict if two patches can be reordered with the same final result.
I have not used Pijul a lot, but I did use Darcs before Git. Some of the merges felt like magic.
Git is fine but it can get messy with complex branching and merging strategies. Patch based systems are intended to improve that.