The installation document is nice but IMHO you cannot follow it and successful install on a cleanly installed system.
Section 3 says to create a new site using the Blank site template. Section 4 says to configure the site directory in central admin.
If you use the Blank site template to create your site directory, section 4 fails as it doesn't recognize the site as valid and says "Specify a URL to a site that is using the site directory template." This in itself is impossible without customization
because while the site directory template is there, it's hidden and the webtemps.xml file must be manually edited to expose the template in the UI. Also the Site Directory template is deprecated and disabled for a reason (otherwise why would MSFT hide it?).
So if the directory template is disabled and hidden, is this a viable solution on a go-forward basis? I think it's a great feature and most companies have a site directory to catalog all the sites. For whatever reason MSFT chose not to continue this model
but why? Do they want to discourage it (if so, why is the Site Directory option still in CA?) or are they going to kill it off and break this feature because they prefer to offer some other kind of directory?
You might want to update your documentation to describe how to re-enabled the Site Directory template and direct people to do that.