I got tired of having to "rebuild" my functions.php (which I use extensively for Gravity forms, etc.) everytime I upgrade HeadwayTheme with the "one-click" upgrade (which I think is great, by the way) so I started keeping my custom code "outside" the headway theme path (in a folder called hw-custom) and then have a little script I run after upgrading to add the included two lines of code after the "Headway::Init()" line, currently number 20 into functions.php and thus including my custom code in the upgraded theme files.
Could you perhaps make something similar a standard feature?
/* Add my custom code */
require_once get_theme_root() . '/hw-custom/functions.php';