yes on docs it works like this, but I am assuming @mdo is planning to remove extra class (.alert-warning). For reference review : http://getbootstrap.com/customize/#variables-alerts

if you review it, it will show whats the planning for this change (but if you compare these variables with variables.less file you will find these variables doesn't exist there, that's why you don't see any change in docs or generated css file (available in source, not referring to customizer generated css).

If you review my pull request related to this code you will see it.