Here's where the css for styling the wysiwyg editor iframe is supplied to sceditor. It could certainly be set up where it checks the variant for a local css file and not finding it uses the default. Or simply just require a variant to have a version of this css file.
$("#', $editor_id, '").sceditor({
style: "', $settings['default_theme_url'], '/css/jquery.sceditor.elk.css",
So that's why a changes the custom.css doesn't help. It's not being passed to that iframe.
The classes for colors is a good idea.