This article seems to be well-meaning but contrasts with the de-facto standard way of storing dotfiles. The Linux Filesystem Hierarchy Standard is quite unambiguous in how it specifies that the purpose of $HOME is to store dotfiles.
https://refspecs.linuxfoundation.org/FHS_3.0/fhs/ch03s08.html
FHS also specifies that applications can store their dotfiles in subdirectories, and this is leveraged by other standards like the Freedesktop's xdg-user-dirs spec to default to ~/.config
https://www.freedesktop.org/wiki/Software/xdg-user-dirs/
I'm not sure what's the point of arguing against the standard way of storing dotfiles while basing the remarks on no standard or reference.