I agree that if you're using HTML5 boilerplate or similar it shouldn't be something you include from gems. Boilerplate is somewhere to start, it lets you get a sane set of HTML5 defaults and a normalisation css. If you're using Twitter Bootstrap you similarly get a grid framework and default styles.
You should definitely tear them apart and change things.
The way I normally start a new rails project is:
1. Copy HTML5BP index.html into layouts/application.html and then add yields and asset includes where I want them
2. Copy Modernizr into lib/assets/javascripts
3. Copy HTML5BP normalise.css into lib/assets/stylesheets
4. Modify my app/assets/javascripts/application.js to include modernizr first
5. Modify my app/assets/stylesheets/application.css to include normalise first
Then as I go along I further customise, remove and add lines to the layout.