The content map is the dom, no? I can't see what you described ending up any less complex than what we have today.
The current split is CSS is presentation while HTML is content + structure. Unless I'm misunderstanding, this proposal would separate content and structure. I'm not sure where presentation would go; you could certainly make a case for it being grouped with either.
There's also plenty of questions around what's content and what's structure and what's presentation. For instance, a section heading is potentially all three. I personally would probably go for grouping presentation with the content, and call structure "layout" to disambiguate it. A section heading is maybe structure, but it's definitely not layout.
A tree node structure for mapping content seems like it'd be the most efficient in all the ways I can imagine it.
How the panes are laid out could be accomplished through any number of methods. Absolute, flow, flex, grid, constraint solving... Or even parent panes using different methods for their sub-panes!
The point isn't to flatten the layout. The layout can be as complex as desired. The point is to remove content from the layout; a named mapping is just an easy way to associate content to layout panes for injection.