I personally prefer a separation of system and my own userdata (e.g. for backup and/or reinstallation), although I also have to admit that most of the contents of ~user/.local are not really user content. Currently (see Strange misbehavior of selection in gnome applications and the linked thread in that post App Center Issues) my normal user seems to be corrupt, but I dare to reinstall EndlessOS since I fear losing some of my configurations/data. I am currently using in general a user test, but execute some applications (e.g Thunderbird, DistroBox/podman) with sudo su - bernhard …
I have no clear idea, where and how ThunderBird and podman store their data.
Regards and thanks for the guidance, Bernhard