Different typefaces have different functions. If the goal is to be able to properly align/indent/space complex texts on a text-only site, a proportional font is not only ugly but actually unusable.
Any typesetting system or a good text editor will happily indent and align proportional fonts. Browsers can indent, but cannot quite align; they lack tab stops and tables are not quite a good substitute.
But it has to be separate from writing. I'd say the benefit of monospace fonts is that it is easier and faster to type and more or less typeset at the same time.
I don’t think the article means to prohibit CSS (or tables) for layout. It is using text markup, and has a footer with CSS padding as well. Proportional fonts are perfectly compatible with aligning and indenting. Look at Craigslist for example.
