The issue I have with yadm is that, unlike stow, it can't manage directories.

For example, if you want to keep track of your whole Firefox profile's directory (without bothering adding/committing single files), in stow it's as simple as symlinking ~/.mozilla/firefox/<profile_dir>.

For programs whose configuration you know intimately this is not a problem (e.g. for bash, we all know we probably just need .bashrc), but not all programs rely on a single flat configuration file.