Why should you use theme(), rather than calling the theme functions directly? Why should you use theme(), rather than calling the theme functions directly? 

theme('box', $title, drupal_get_form('comment_form', $edit, $title));


Why doesn't the code call the theme function directly, as in the following code?

theme_box($title, drupal_get_form('comment_form', $edit, $title));
You have to use the theme() function for the override system to work. For example, your theme may override the theme function for a module, or a template (.tpl.php) file might be used instead.