I forgot to mention that your minimal layout was a very welcome resource for me as I am looking into adjusting the stylesheets to somewhat similar results. I will most likely do so as soon as I have wrestled this flu, which is partly the reason for my derailing, sorry about that… 
As you said, the Custom CSS feature works just like it should and is very powerful. I would simply focus on documenting and commenting the CSS sources or writing a brief reference document instead of developing a wizard to customize site appearance.
I haven’t really been looking into the CSS for more than a few hours, but many of the trivial changes have been frustratingly difficult to track down and implement just by myself.
Edit: Visual finish of a forum might not be what discourse is about, but Discourse is still very appealing to several audiences that value, at least to some extent, appearance over perfect ergonomics, such as designers and online gaming communities, of which latter are the ones most likely in my opinion to benefit from Discourse’s features.