Good luck sorting out the dotfiles standards on linux. Many projects doesn't even respect XDG_CONFIG_HOME. But if you use it for your own applications and you like it it's fine, I've seen worse (looking at you thunar).

I think many of us who are annoyed by the whole dotfile mess on linux, have some sort of symlink system, be it with stow or just a script (personally i have a list with relative paths to a bunch of configs in a git repo that are often renamed and the target path in column 2- , that i parse and symlink, create dirs and stuff in a script). I don't think this issue will ever be sorted out, and it's not that big of a deal, as long as it is DOTfiles/dirs and not normal visible dirs in ~. Sometimes i wish I had a single (+root) user system, with no /home/* directories at all with configs in /etc etc ;)

One disadvantage i see in your system, is comments. I kind of like to add chunks from the man page in some configs or just making sections in long files. Another is getting an overlook of the values, since one would need to read the files to see the values (if they aren't boolean).

Nice webpage and blog, subbed and saved.