I don't think it's wrong. And it's currently the only way how to build a multi-option theme. (I just don't like the [theme:parameters] approach since users can destroy a theme when used wrong.)
And yes, the theming settings for TinyMCE only allow one CSS file to be set. My customers are fine with the following:
Theme for the frontend, Barceloneta for the backend
Base theme CSS for TinyMCE (so structures are visible)
Additional color for frontend
The only current alternative is to have your CSS rendered from a view which then takes your color choices into account.
Is there another way of setting this option (not define it in manifest.cfg)?
Where 'does TinyMCE get the css from' ?
Can I set it in the registry or can I somehow make a diazo rule that loads a CSS?