This really has little to do with WP. Processing of that file is simple inclusion, I don’t see any complexity to it.
Relevant code from WP core:
// Load the functions for the active theme, for both parent and child theme if applicable.
if ( ! defined( 'WP_INSTALLING' ) || 'wp-activate.php' === $pagenow ) {
if ( TEMPLATEPATH !== STYLESHEETPATH && file_exists( STYLESHEETPATH . '/functions.php' ) )
include( STYLESHEETPATH . '/functions.php' );
if ( file_exists( TEMPLATEPATH . '/functions.php' ) )
include( TEMPLATEPATH . '/functions.php' );
}