Google has clarified its help documentation for the new site name markup and old favicon requirements about if they can be specified on the domain versus sub-domain versus sub-directory levels.
In short, site names are supported at the domain level, and not at the subdomain or subdirectory level. Favicons are supported at the domain and subdomain level, and not at the subdirectory level.
Here is a screenshot of the Site name docs (click to enlarge):
Here is a screenshot of the Favicons docs (click to enlarge):
Forum discussion at Twitter.
