Question about functions.php

Accoding to the codex this loads before any file (correct me if I am wrong), so How is it that frameworks are able to create a custom-functions.php and those functions in there are run, before the rest of the theme?

Example,

Lets say in my theme framework I have some pluggable function

if(!function_exists('function_name')){
    function function_name(){}
}

If in my functions, or custom-functions.php I define that method function_name(){} every thing works out and is happy.

How ever if in my functions or custom-functions.php I say:

require_once(‘path_to_file.php’) where path_to_file contains the definition of that method function_name() I get an error. Saying it was already defined in such and such file on such and such line.

Yes I can define it in the functions.php or custom-functions with no error? I just cannot link to a file, in the functions or custom-functions that defines it?

why? if the case is, that the functions.php or custom-functions.php runs before any theme file then the fact that I am linking to a file that redefines the method should not be an issue.

thoughts?