Manual:Wiki in site root directory

Why to, or not, use the root directory of a Web site as the wiki directory.

Template:Wiki-in-docroot links here and is used in Manual:Short URL. Details needed below.

Wiki specific domainnames or subdomainnames
I like these two examples for sites that are predominantly wiki. If wiki is to be the dominant paradigm of a site, then no special wiki directory is needed and to use one is redundant and counter intuitive.
 * http://wiki.example.com/Article_name
 * http://cookbookwiki.com/Main_Page

Why should above be deprecated? Please be specific, of course.

Frankly, I'd agree. There should be better guides to getting this to work - I've tried everything on this site, including the Mediawiki type one (which I wouldn't prefer, but would be better than the huge and ugly URL I'm getting at the moment - /mediawiki/index.php/Main_Page is a huge waste of space when I only need /Main_Page for my site.