The point is that these are all interchangeable, but that best practice is probably to use none of them unless it really improves your comfort level with the OS. “Ignore the GUIs” is indeed getting directly to that point.
You choosing to not believe that is a separate matter.
I can’t read your mind and it’s honestly still not clear that you understand: these software all read and write to the same database. There isn’t any “configuration” to make them do otherwise - other than using Shelly for flatpaks and appimages in addition. And Shelly isn’t a source of truth for flatpaks either.
Just use (or don’t) whatever you want. Preferably pacman + paru if you use AUR for greatest reliability.
Note: per the commit referenced below this is likely moving - at least officially - to shelly. It’s up to individuals to decide if they feel shelly has sufficiently stabilized.