Are you saying that if a theme designer used "<?php wp_head(); ?>" then the specifications for that are somewhere in functions.php?
wp_head is a hook.
if you want to see just what core stuff depends on it, look inside wp-includes/default-filters.php
add_action('wp_head', 'wp_enqueue_scripts', 1);
add_action('wp_head', 'feed_links_extra', 3);
add_action('wp_head', 'rsd_link');
add_action('wp_head', 'wlwmanifest_link');
add_action('wp_head', 'index_rel_link');
add_action('wp_head', 'parent_post_rel_link', 10, 0);
add_action('wp_head', 'start_post_rel_link', 10, 0);
add_action('wp_head', 'adjacent_posts_rel_link', 10, 0);
add_action('wp_head', 'locale_stylesheet');
add_action('wp_head', 'noindex', 1);
add_action('wp_head', 'wp_print_styles', 8);
add_action('wp_head', 'wp_print_head_scripts', 9);
add_action('wp_head', 'wp_generator');
additionally, plugins use it.
you can create your own similar hook and move stuff around.
Thats what Ive done..