Of course, it depends a little on how you define"Design". Maybe the term suggests many and very broad capabilities to you, but I think it's restricted to collecting and positioning imagery, texts, animations, etc. in a free but also effective and efficient way. So it's not a one-stop-application for all the website's content. We still need other applications to create and edit a lot of components. Just like InDesign, which still needs word-processing, Photoshop and Illustrator (among others). But we could and should stop doing layout in Photoshop.
(Oops, I hit the Save again too soon...)
And about the HTML: Muse doesn't work directly in HTML. It operates in its own file format (the .Muse file) and generates HTML when we export it. (In fact I think there's a lot of other stuff being published to BC than just the same exported HTML.) So any change in what is or will be the generated HTML, needs to be translated back to Muse its own file format to keep track of it and let you preview what it looks like. Apart from whole autonomous 'chunks' of HTML which can already be added, more integrated changes which affect other parts of the content as well (like CSS, Scripts, etc.) are impossible in this approach. Therefore, it's a one-way direction. You can change the HTML, but you'd have to do it very time after Muse exports it, and there's no way to push such changes to BC.