Again, the contradiction is still there. The issue is that "no regular user" should care about IPv6 yet. It's simply a non-issue to most regular users. As you yourself stated, most people don't know what IPv6 is and it therefore does not affect them. You've listed 4 ISP's of the hundreds that exist. At least one of those (Comcast) is opt-in and (it seems) invite-only, therefore, once again, users must still *care* about IPv6 to have it. They still need to jump through hoops (6to4 or some explicit ISP support) to get it working. The 99% of users Khaled quoted trump any presence IPv6 has right now. All IRC networks have an IPv4 address, even though individual some servers may be IPv6 only. There really is no reason to use IPv6 *unless* you care. Simply put: very few users need this right now.
As you said, if your computer has an IPv6 address that is connected to the internet, Windows will resolve IPv6 addresses. mIRC will too, except in mIRC's case, "having an IPv6 address" means binding to your IPv6 adapter rather than your IPv4 adapter. This step is necessary because even though you may have IPv6 available (and by your loose definition, "enabled"), it does not necessarily have connectivity. As Khaled mentioned, typing /server irc.ipv6.xs4all.nl may resolve the hostname to an IPv6 address (2001:888:0:2::6667), but it will not be able to connect unless you explicitly enabled that underlying layer. To a "regular" user, this is confusing. Therefore, mIRC warns you about having that layer on and makes sure you know what you're doing so as to avoid confusion. I see this as good user interface design.