[pizza234]

There's no limit to where applications can put their files, and this applies to any operating system, so complaining about, say, version managers has nothing to do with a given operating system.

If you take Windows, you're going to have %USERPROFILE%.pyenv for example, when it comes to Python (pyenv).

It's unlikely, but not impossible, that a binary ends under /usr/lib, since it wouldn't be in $PATH. If it's there, it's likely invoked via a script somewhere, and this is not good practice, and again, not inherently Linux.

$HOME/.local/bin is not good practice, for the same reason (not being in the standard $PATH).

$HOME/bin seems actually a good place for placing user-specific binaries, since there must be one place for them, and I think it's a proper place.