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I think (?) it’s generally true that the root user should never mess with users’ files.
Imagine your home directory is shared across many systems on a network (my alma mater did this). It would be really bad if a sysadmin for alpha.university.edu removed a program, and suddenly your personal settings were removed from beta.university.edu — even though that computer still has the program.
This is one of the “UNIX on the desktop” issues — a lot is designed for a sysadmin/multiuser situation, and it has some gotchas when using it as a desktop machine (I’m used to/really appreciate the directory structure and settings management at this point, but it may take some getting used to).
I always say I have a 1969 Wayne Industries Batmobile. Usually a sheepish, “oh, um, we don’t cover that, sorry. click”