I spoke to Andrew Rothery of Tru-Life Adventures, who wrote the letter questioning HalfPixel's ownership of the webcomics.com site (see articles below), and he explained his conclusion:
Brad Guigar's public remark that HalfPixel had "acquired the rights" to the URL aroused his suspicion. Why not say "owned" or purchased?"
Andrew: "A quick Who Is lookup revealed that the new contact information for the site was PA (that's how it's listed, just the initials) and Robert Khoo up in Seattle. Since Robert's the business manager for Penny Arcade, and Kurtz is friends with Jerry and Mike, much of it fell into place. If nothing else, the Penny Arcade folks seem to be be in a much better financial position to afford such as apparently overpriced domain."