As for the solution not existing yet - as people pointed out there is tar, zip, git, and shar which all seem to accomplish the same thing
I have no idea how someone could read such a thorough README and say "this sounds like a solution looking for a problem" with a straight face.
Is visibility into what's being created a problem?
The listed problems like "everytime the template changes, author has to rezip and reupload the folder" don't seem to be solved with stamp to me, it seems like the problem is now shifted to controlling a version of this new format and still distributing it somehow (probably through git) at which point you ask yourself why can't the git repo already have the structure? If somebody wants to rename something they do this really easily, no need for var substitution.
If there was a migration mechanism that would move files from an old template to a new one I would see value added.
It makes find and replace across all files trivial with your editor, whereas that would be less fluid with a zip.