I put them in a dotfiles directory and use `stow`[1] to symlink the contents to where applications expect them to be. Under that root I have a home folder that it is symlinked to `~/`, and I have and applications one that is symlinked to `Applications Support` through the `-T` argument of stow.
To this day I still have to find anything that has problems taking a symlink instead of a file.
I am pretty happy with this setup as it means that all my dotfiles are in a single root folder that I manage through a git repo.
So I don't see what the linked articled means when it says that stows "makes (unsurprisingly) no effort to support ~/Library/Application Support.". It is literally a bit of organization from your side and passing a flag.