Recreating a path to original locations is a way to configure stow.
You can utilize bash to automate it. Mkdir can create entire trees in a single command.
After links were created you start using your configured software.
It’s a link farm built using a packaging system. You put your configs into a “package” and then link said package where it belongs.
Git is useful not as a combination for stow, but a standalone way to version control your configs.
For nonidentical devices you create additional packages prefixed with specific device name. You don’t need to link all packages at once with stow, pass a name of a package to link it alone.