Actually I believe you're starting off on the wrong path right there. PageRank is determined only by the links leading to the page. It's page-specific, and is not determined or affected by the PR of the site's home page -- other than that a link from that home page will pass some PR to the page in question.
If you add a page to the document root of a site it will tend to have the same PageRank of the other pages there because it will also tend to be integrated into the site's navigational structure the same way -- that is, it will have the same backwards links.
If you move a page from the root to a subdirectory and maintain the same linking structure, the PR of the page will not decrease. The directory structure isn't a factor.
Part of the confusion may be because of the so-called "toolbar estimate" of the PageRank of newly-created, still unindexed, pages -- which does seem to be determined by the by the index page's PR. But that's not actually the PageRank of the page, which in that case has not yet been calculated.
As for the point of your question, I agree with Yidaki that using "3rd level domains" causes those sets of pages to each be treated as separate sites for PageRank purposes.