I can see your point, but you should also realize that the theme only refers to presentation and website-specific function. So generally, unless you are creating an all-encompassing theme to use on multiple sites, then the theme is going to be pretty customized anyways.
If you really want to keep Roots updated, I assume you’ll agree that most of the markup and CSS would be ignored in updates, since this is a base theme. You could avoid modifying the Roots functions and sticking to adding new functions/classes to the custom.php file or creating your own php files and keeping your updates there. Then you could diff the lib folder once a month and see if there are any updates made.
I know you say that’ll be a huge time sink, but really that’s the option. Keep in mind, this is a starter theme, which means you use it as a base to create your own completely custom theme. It’s not anywhere near the same as modifying core Wordpress files (which nobody would suggest you do).