I'm developing a child theme, but also want to make it possible for that child theme to have a custom functions.php file that won't be overwritten during theme updates .. is this possible in any manner?
You can add a custom functions.php to your child theme. As long as it's in the child theme folder, it will not be overwritten when you update the parent theme.
See http://codex.wordpress.org/Child_Themes. Read the section "Using functions.php"