Those are kind of out of scope I think, it's designed to just pull the threads themselves, not forum topic indexes (which will likely be in a future build).
I'd have to see how you're calling these extra pages (header/footer) to be able to give a for sure answer.
I'm pretty sure that I could make an index page which could take all files in a directory and build a sitemap for you; but keep in mind that if it's just a custom header and footer that google won't really care; you're not feeding your content to them, you're simply feeding urls of your threads to them; the feed does not include any post content (as they don't want it).
Another product i'll be coming out with soon is a simple sitemap lister that you can manually enter urls on your site; but I'm working on a couple of other projects until I can get to that.
I've been toying with Curl for building automagic sitemaps, I have something that works for the most part, but you have to think that php has an execute script limit which would make it die prematurely on large sites (or forums for example).