Not at all. You can 'git add' (or in the case of the technique above 'config add') only the files and folders that are safely stored in a repository. Because of the 'ShowUntrackedFiles' flag, git/config won't always show folders you don't want to track, which would be annoying.
Working on it! I'll give you full credit for it and link to this thread for reference. Also let me know if you have a Twitter account you'd like me to reference.
Honestly this is genius! I hadn't thought of doing it like that, thank you! I had resorted to the usual .cfg folder and a helper script to link/update everything.