I think you've just hit the nail on the head as far as my biggest issue with this project. The documentation lays out an install method that should be roughly followable for anyone (though it needs a bit of fine tuning here and there) and then the rest of the configuration guide and documentation assumes that you have installed the software in a completely different way and doesn't work the same as the guide laid out.
The documentation should be uniform, if you want users to install it one way then write the guide and documentation so that's the "default". Sure present alternatives or notes "if you've installed via git, your commands will look like this xxx" but ultimately the biggest issue I've had with getting this deployed is inconsistent or lacking documentation.