The goal behind my template here was to provide a solution to a very specific request in how to display blog posts on the home page, and that was by gathering current posts from a typical post loop and then listing them by category. There are ways to modify it to display only certain categories and whatnot (i.e. query_posts()), but in regards to your request, assuming I understand it fully, it lacks in a couple areas, primarily in setting up 'static' category sections on a page.
If you have WP set to display the lastest 5 posts on the main (home) page, the template calls those 5 posts as normal. It doesn't concern itself as to which categories those posts are in until after it starts displaying them. We could certainly restrict posts to the categories you prefer, but if you want to assure exactly three categories are displayed at all times, the template fails you there.
So, if you need 3 categories at all times with 1 or more posts under each, the use of conditionals and whatnot with a single standard post loop won't help you. Not unless you're bothering to make sure the current N posts are always in those 3 categories... That's why I believe setting up 3 different post loops with query_posts() initializing each (to define the category and post count for each) is your best option.