Have RW pages with no theme or extra code applied

I have to manage 2 separate RW files right now for my site and would like it to be one. One file has all of my Site pages using foundation and stacks. The other RW file contains only HTML pages that are called using php include statements into my master pages. This setup allows me to just change out affiliate ad code without having to republish the entire page. They are separate because my web pages that get published from my master file contain all of the theme and code from the general code sections while the RW file with HTML pages has no theme and no extra code so they can be published clean.

The feature I want goes beyond the current “turning off the theme” checkbox. I also want to turn off all general code as well on specific RW pages.