The template include system doesn't go through the request processor so whatever we do for resources won't impact includes at all. You can use [ad_package_root_dir package_key]/includes (or /lib or /templates or whatever we end up with) to get to your includes.
I'm nearly done with the /resources/package_key implementation and will write a simple package called acs-resources to mount at /resources which will make them appear in the site map, too. This will make them seem a lot less "magic" ... we'll be shortcutting processing of a particular node rather than inventing it out of thin air.