Are you really arguing that alignment, consistency, appropriate typography, non-mediocre use of color, and more broadly, overall usability are only relevant to 1% of web users?
Overall usability is what the other 99% care about. And should be of primary importance.
Saying that overall usability == "alignment, consistency, appropriate typography, non-mediocre use of color" is just not true.
Usability is one type of design. Those are another. They are not synonymous.
You may say that these factors aren't noticed by the 99% but have you ever heard somebody utter the phrase, "I don't know what's wrong with this, but I just don't like the way it looks?" That's a "99% phrase" but it comes from a very real place and can be easily avoided.