Now, this is using Alexa and I'm not going to pontificate about the value in using Alexa to judge popularity however, I would consider XKCD far more nerd-centric than PVP is.
I will say that when the only value proposition you have is giving something away free, and then you hide it behind horribly dramatic blog posts, ads for said 'free material' bound into a new medium, links to 'other projects', and other fluff, you're not doing something particular business savvy.
At least PA has the excuse that they are more interested in becoming a media company than a webcomic company. Or at least that's the only thing I can assume when their front page looks like this:
That's a great teaser for their latest comic!
Now, I'm no webcomic artist. But I am a marketer and a technologist. If adding a bunch of 'brand' to your website:
1) Hides your webcomic
2) Increases server load
3) Increases bandwidth costs
4) Potentially increases advertising revenue
I would hope that you've got a strong business case for doing so. As it is, I can cost Kurtz a shit tonne of money by installing ad block and visiting his website on a regular basis, increasing his costs with no measurable impact to income. And as he makes the comic less and less integral to his site, the less I'm inclined to even bother going there.
Let's call it "the Laffer Curve of Webcomics". Net income will increase as you market your "business" more and more on your site, until the content is overtaken by the framework, in which case you're paying increasing infrastructure costs to remind people you still have a web comic.