I think an issue I have with it is if I want to move the configuration to another place, the only way I can do it is via a symlink. If applications used the variables above, you would be able to easily organize things differently if you choose to.

This would also allow you to test if something there is causing issues or if you wanted to format and reset things. Just delete that directory or set the variable to another path.

I don’t set ls to ls -a, but sometimes I create hidden folders and files on ~/ so it’s not distracting. Scanning through a lot of things because everything is dumped there is a mess.

Indeed, without env. var we are stuck with ~ "madness"

I do the same kind of things actually. I do not have ls alias with -a flag, and I do other thing like you mention, too. You are not alone here.

I rarely type ls; I have l aliased to something like ls -lAhFvN