I don't think it was deliberately misleading. While it'll work for any site if you know what you're doing, the instructions are for making it work with Github

I don't think it was deliberately misleading. While it'll work for any site if you know what you're doing, the instructions are for making it work with Github specifically because of the paths involved. Without this, some people may have trouble getting it working on Github. On your own site, you likely wouldn't use a subdirectory, making some parts of it simpler.