I'm just starting the development of this script, so the only reason I have it inside the web tree is for simplicity of my own use during development. I had considered having it there on completion to make the installation of the script dead simple (copy the files, chmod 1 thing, done).
It's not that I can't put it outside the web tree. I was just looking for an option and wasn't sure how much real security the .htaccess file would provide. I'd seen it done before with another app and was intrigued. :-)