I don't know if Tim Berners-Lee thought about layout. SGML was text with semantic information, and HTML was text with cross-references. Back when displays were tiny low-resolution things little better than terminals, and most web pages were just text with a few images, layout didn't matter. It was all ugly. Now that displays are larger than books, and pages are heavy enough to contain the entire Gutenberg Bible, people are starting to care.

Maybe in 5-10 years, with enough server-side computing power and bandwidth, sites will ask for the client's screen size and desired font size, then serve an appropriate PDF.