Yup! I can confirm that the add/remove operations don’t exhibit this behaviour. One of the automated operations I was performing was clearing one or more collections before rebuilding them (or creating them). I think it’s still unexpected that there are operations that automatically commit themselves, even if you’ve set that option to false in project settings. Creating, renaming, and emptying are all things that we do via automation that we don’t want to spam the repository with. We still want to mark collections for add and check them out, but automatically committing changes and bypassing our normal preflight checklist is a big problem for us.
I was rather excited about having a setting so that I could stop maintaining this divergence, but I don’t think it will serve our needs as-is. Simple enough to port over when we upgrade to 5.6, so thanks for the heads up!