Just FYI, the master branch is pretty old, so as I'm sure you've discovered, the diff between that and native-boot has a fair amount of extraneous crap that won't be relevant for getting the VE patch done.
I recommended diffing from mini-boot because it's the cleanest diff which still gives you the information you should need -- over time, as the branches have evolved, we've gotten progressively more general, so the changes between bootloaders has decreased between each new board's release.
I really am sorry that this is the state of affairs. All of these branches really need to be replaced with a single one where the appropriate header gets included for the board you're compiling for, just like libmaple. It just hasn't gotten done mostly out of inertia and lack of developer time.
In any case, please do keep us posted as you go.