Drupal comes with a lot(!) of predefined markup & css.
Modules are adding styles and markup to the themes and so themers have limited control over whats going on inside the theme - that works well for some themers - others not so much.. or to put in other words:
"WTF does all this bib markup do in my bib site - aaargh for bib sake, Gimme lean mean mother bib 'ing markup"
The Mothership is a theme thats build in the opposite way normal drupal practice: clean out "useless" markup & remove classes that clutters op what should be beautiful source.