The problem is, in order to be valid HTML, in order to comply with current standards, and in order to display properly in all browsers, the last thing on the page should be:
</body>
</html>
The current Moodle distribution leaves out those closing tags on most genertated pages. Granted, using the current out-of-the-box product, it's a simple matter to add them to the footer.html file (Since they should be there already, what was the motive in leaving them out?)
As to "why would you use print_footer() anywhere else?", any piece of html code is just that, and the more those pieces are free to be moved around within the framework of the page, the more the program is able to be customised to the individual site on which it's being used. In the themes forum, you indicated that you are working toward separation of content and design, and it would be a logical step in that direction to not have the $loggedinas and $home content tied to the closing body and html tags. Suppose, for example that I want the loggedinas string to appear at the top of the page beneath the banner or at the top of the right hand column. As Moodle now stands, that would take major code revision. Even to move the current footer.html content inside the bounding border on my site so that it's centered with respect to the center column and not with respect to the page would take considerable code change. (see http://every-nation.com/exam/ The site is being reworked toward total CSS definition, including the position of the columns. Try resizing the browser window and you'll see the benefit.)
No malice intended I assure you. Overall, Moodle is very well done in my estimation. I don't know PHP well enough to do more than hack other people's code, and my entire site relies on open source, so I appreciate your efforts. However, in the evolution of Moodle, there needs to be more separtation of content and design. As it stands, I won't be able to easily upgrade my site to the next version of moodle because I've made so many changes to the html within the files that I'd have to start all over again. That's the reason I suggested you take a look at ezPublish where php and html have been nearly completely separated. I thought you might get some ideas as to how to more effectively accomplish that task.
Sorry for the long post, but I wanted to explain my thinking.
Thanks again for Moodle, and good look with your thesis.
RWW