i feel like using GNU stow to manage your dotfiles has always been a hack.. has it ever been a supported usecase?
stow is an indispensable tool for me to manage /usr/local for manually installed software. my workflow goes:
./configure --prefix=/usr/local/stow/myapp
make && make install
stow myapp
now, myapp and all its supporting files are in the right place in /usr/local. if i want to "uninstall", i just run stow -D myapp