Oh wow - this is incredibly helpful! I have been working on some shell scripts to do this over the last week and just replaced the majority of the script with GNU stow and it is much more elegant in its simplicity. Kind of surprised I have not heard of this tool.

Using https://github.com/Czahrien/shell-config-files if you are curious. I settled on having a main dotfiles folder containing packages that will always be stowed, a platform folder with a name derived from uname -s -m and a host folder derived from the hostname.