You can have a separation of presentation and content while still targeting a specific medium, the separation doesn't automatically mean that the content is fitting for every medium.
And the elements used here show that pretty clearly. When just regarding HTML and ignoring CSS, you can see its elements that are made for other mediums than paper. It is Hyper Text after all, not Text.
And when just regarding CSS, you have all those elements that are of no use on paper, like position: fixed.
Or just think of the issue in responsive design of wanting to have another, shorter text for mobile devices. There, even the content alone is not fitting for the medium, regardless of the presentation.