You could create all your own templates in a child theme but the core engine does contain the HTML tags and ids. For me this is the problem with Theme Frameworks (Unless your willing to totally commit to them).
The code quality is outstanding but it's just too much work to roll things your own way. Just to remove the the genesis and studio press links in the footer you have to write a function remove 2 filters and add an action.
To replace all the divs with your HTML5 tags your going to have to have to write your own functions for
add_filter depending on the situation.
You can use the visual markup chart to help with your efforts.