Old thread, but I've been unable to modify the current version without changing core files, so...
Most people want to change the header and footer. Since a forum is usually part of a larger site, there needs to be an easy way to change these areas (e.g., for links pushing back to the main site, etc.)
Structure the templates so there is a head.html, header.html and footer.html file shared by all template files.
Since a forum is often part of a larger site, it is convenient to be able to share those files, so the ability to "include" their contents (e.g., via PHP INCLUDE or similar) is nice. That way, there is only one file to maintain instead of having to manually edit contents in various apps part of the same site.
To prevent overwrites during upgrades, two approaches could be used, or both.
1. The above files could be part of the root directory of the install, and 'included' (if present) at the proper points in the templates.
2. They could be located in the templates directory, but a different directory can be specified in the config file. (To prevent upgrade overwrites, one would copy/rename the theme directory and point to the non-non distro location via config.)
These are such common techniques that I think most of us can figure out how to modify the header and footer areas in applications without even reading any documentation just by looking for such file names.
As for favicons and changing the layout of the forum, that sort of stuff doesn't interest me so much as being able to just easily make, and maintain, header-footer changes. I think the current design is superb and allowing changes to it would probably just result in confusion, to both maintainers and users. You could do similar to Phorum and allow color code changes to be made in a settings file.
head file gets included just prior to the closing HEAD tag.
header file gets included immediately after opening BODY tag.
footer fle gets included just prior to closing BODY tag.