Generally speaking, Roots is meant to be a starting point for a highly custom theme. What that means is once you start a project, it’s not really Roots anymore, its whatever you make it. It’s not really intended to be a “framework” or “parent theme”, which is why we generally suggest that it not be your first theme.
That being said, the thread I linked to above has some general suggestions on how you can do this. For a minor point update like 7.0.1 to 7.0.3, you could easily just look at the commits and implement anything that you think is important for you. Usually when we use Roots, we don’t do any major changes to core /lib files, and try to keep everything in our own custom php file that we just include via
extras.php. There is not a lot of CSS/LESS specific to Roots so your designs shouldn’t be impacted. Same should generally go for JS or Template Partials too.