"You can't change the crawl rate for sites that are not at the root level—for example, www.example.com/folder."

What if Googlebot starts at a non-root location (via a link from another site)?

Will it always start at root?

I think they just mean that it's a whole site/domain action; that you can't change crawl rate for a sub-directory based site ala Wordpress MU/Multisite with directories.