Skinnability is a pretty superficial sort of view customization. It's no stretch to imagine a system that would be skinnable and still not have proper separation of concerns; indeed, I would guess that many web apps qualify. Just beacause you can juggle fonts with CSS doesn't mean that mixing and matching different chunks of data on one page comes easily.
Separation of concerns is important, but I don't see the point in attempting to coerce existing systems into a model. Why not just look for the separation of concerns instead?
Because there's more than one way to break up a web app to the the MVC model. In fact, in something like a blog, I think one could make a case that the database is the model, the HTML/CSS/browser is the view, and the scripts on both the server and the web pages are the controller. But what does that prove? What does it mean? How is that observation useful?
The main use I can see is that the view and controller are broken up into multiple disparate pieces and are consequently a huge pain to deal with. That is to say, web applications do not follow a clean pattern, aren't particularly well-designed, and that they've succeeded in spite of that, or because they have other advantages.