Currently, the Style Manager only allows one to clean up all unused styles. Some of these styles might be needed when adding Selected, onFocus, Hover interaction via code (not currently available natively). The ability to clean up specific unused styles would be a great help around this issue.
The problem is however when you export the site, the unused style are still there just that they are not tied down to any elements.
I personally solve this by making web page for the purpose of collecting styles I never want cleaned up. I add divs and assign them the styles there and this workaround works for me just fine.