I find it easier to exclude all .* from the rsync I do to synchronize documents/data etc, and exclusively manage the dotfiles through another program, homeshick, where instead of making exclusions, I make explicit inclusions. The config files I care about are far, far fewer in numbers than the random crap programs spew in dot folders.

I like the XDG specs, but even programs that pretend to follow it don't follow it. CMUS, a music player, moved into ~/.config.. moved everything, including files that belong to .cache and .local/state. Google Chrome has 999 mb worth of files in its .config folder on my computer. The truth of the matter is that XDG only managed to encourage developers to move their files away from the root of $HOME but they didn't manage to make people respect a proper hierarchy of files.