I do something similar to what you're describing but it sounds like you have way more styles than I normally do.
When I setup a new style theme, I go ahead and build out all of the really common UI components and their variations. Ex: btn-default, btn-hover, btn-selected, btn-disabled; menu-bkgrd, menu-item-default, menu-item-hover...etc.).
After that, I try not to deviate from those standards across the entire design. If I need to, I create a new component and style that: toolbar-btn-default, toolbar-btn-hover, etc.
So I never have an "alternate style" for a component, just specific styles for specific components, if that makes any sense.