Multisites at different directory levels

I think you are confusing the multisite concept of subsites being divisible by ‘subdirectories’ with any actual files existing in subdirectories in the webroot. Nothing changes in the file system that you might notice as the term subdirectory in this usage is just a change in the URL.

On a subdirectory install, all new sites will be created as subdirectories of the root domain name but there aren’t any subdirectories created physically on your server as you might otherwise expect.

This is all done in the mapping system where a new site will be ‘mapped’ to the ‘domain with subdirectories’ you want the site to ‘appear’ as. Thus you might have something like…

http://WWW.MyWayCoolwebsite.Com/ICantBeleiveThisWorks/

And even

http://WWW.MyWayCoolwebsite.Com/ICantBeleiveThisWorks/AsWell/

But you won’t find any file structure representing that layout under webroot.

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The subdomain and subdirectory install types denote the way WordPress considers the way the new site is to be named before mapping takes over and these two ‘terms’ allow some particular magic with sites as they are made under user controls as either a subdomain existing via a ‘wildcard’ subdomain or else what might appear as a subdirectory under the root domain.

The Domain Mapping System then extends those naming conventions greatly.