To be honest, it is quite complicated now as well with all of the proprietary software

For Linux applications that respect XDG? Sure. There are plenty that don't because they either predate that specification, or they just don't care. Linux filesystems are generally much faster at executing reads on many small files, meaning fast search tools like ripgrep and fd make it so I don't really have to care. They'll run through my whole $HOME in 5 seconds flat. There's also stuff like locate, although I don't like maintaining an index. SSDs are so damn fast that I can just rg --hidden --glob '*.toml' 'the_setting_i_want_to_change' ~/ whenever I want.