Re: bbPress 2.0 – Theme Compatibility
@anointed – In a word, no.
WordPress custom post types only know to look for their files in the root of the theme folder, and the same goes for page templates as well. For now if you want a totally customized theme, those files need to live in the root. I did my best to minimize the number of files in the root, and instead split them up into template parts in the /bbpress folder (because I want the same thing you do.)
It might be possible to hook into the template loader, see what the request is, and force it to look into a different folder, but there’s no possible way to do it at all with page templates; it’s actually purposely disallowed to prevent the theme from having to scan every file inside every subfolder to find them.