If you've got the time and energy to keep that 1% happy, go for it. (And most readers of HN may be in that 1%.)
But you should do so AFTER the other 99% are satisfied.
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.
I see what you're saying but I think you're missing the point that though people will generally not be able to externalise why a design is appealing the effect of the design is still felt.
I'd be inclined to agree that perhaps <10% will notice and <10% of those will think that the details attended to will matter. But, I consider that those who are ignorant of the design process and considerations will possibly be the most effected by those changes.
I think you're coming at this from the wrong point of view. Of course, the other 90% (i.e. what the site actually does, its content, etc.) are more important.
But the goal of this tutorial was teaching what I know, i.e. design, and specifically the visual part of web design (i.e. I didn't talk about branding, interaction design, etc.). So that's what I wrote about.