Steve yeah, that is the workflow. I do quite a few customizations to the kit - each month basically. I'm able to start up 3-4 new projects with each new month so its worth the effort. My customizations don't take long to do though either.
I remove basically all the pages besides the style guide page - I add in a Research, Sitemap, Wireframes, Design, Assets, Handoff, Archive pages. I add in some additional frames for favicon, open graph, cover image.