We use 'Default' as our control panel theme and override it. We keep the same theme on all of our clients sites, and often make improvements and enhancements to it.
To aid with this, we adopt the NSM_override method of simply importing an external CSS file from override.css but go a step further by actually hosting it elsewhere (in our case a special domain where we keep this kind of stuff).
This way it takes seconds to add to a new site and all of our sites get improvements at once.
It's never popped up, but if a client wanted their own bespoke changes we would probably import our loader.css as normal but then continue our overrides below, so for example....
All of this is a round-about way of saying that you don't need to comply with the EE file structure to manage your custom themes. You can continue to use EllisLab's images by simply referencing their standard location or you can use your own. Because everybody has 'Default' there's no need to re-distribute.