Work still in progress
You basically have two options:
Add these classes to "static" CSS files: they won't be able to reference flavors, but can use CSS3 properties (as of Nuxeo 5.5 and 5.6, CSS3 properties management is not working well for dynamic CSS files).
Add theses classes to "dynamic" CSS files (see above how to declare new dynamic CSS styles and bind them to the theme page).