I agree, all markup added manually is same as content. If it cannot be derived automatically from the rest of the content, then it is on the same level as conte

I agree, all markup added manually is same as content. If it cannot be derived automatically from the rest of the content, then it is on the same level as content and what we call "markup" becomes simply a special notation to describe these parts of the whole content. A drawing, a formula, a form, and so on. Or even punctuation; it may be important to tell the difference between the period that ends a sentence vs an abbreviated initial :) I myself don't think it's worth to actually keep content and markup in separate files, so for me the only possible use case was conflicting markup, i.e. markup that exceeds the limitations of our tools, something like two overlapping tags in XML. Yet even this case doesn't require actual physical separation; it can be solved with a different notation or maybe a different tool (like SGML, which, I believe, supported overlapping tags).