Sorry if this is a super naive/dumb question, but why wouldn't I simply write a "build" script that copies files out of my dotfile repo to where they're supposed to go?
Replace copies with links and you are golden. Yeah, you can write a simple script to create those links for you, but Stow seems pretty full featured.
2) By using copies instead of symlinks you'll need to run your script Everytime you make changes and be careful to edit only your clone instead of the target location.