The million dollar question isn't our interpretation, it's WotC's. Does their policy apply to the kit only, or are they applying that beyond?
Of course they aren't going to apply the terms of this policy to any sites not using the kit.
That doesn't mean they won't take recourse if a site infringes on their IP in other legal areas - but thus far all the sites they have taken action against have included published material from WotC books that was being freely posted and openly distributed online.
Now, I definitely agree it would be nice for WotC to release a 'statement of purpose' as to what fan sites they have no problems with. But it wouldn't really change anything - as it is, WotC could go crazy tomorrow and try to shut down every site that mentions the words "D&D." They wouldn't actually be entitled to do so, but many sites would probably get hurt due to not having the resources to handle a legal battle. But the thing is, even if they posted a policy saying "These websites are fine"... they could still go crazy, change their minds, take down that policy, and go after fansites anyway.
For myself, I'm absolutely confident they aren't going to do any such thing. They will go after sites that illegally distribute the actual material in their books. But most fan sites, operating under fair use, filled with fanfiction, artwork, characters, stories, backgrounds, homebrew material, articles, reviews, etc, etc, etc? Shouldn't have any issues. Many of those sites will need to make absolutely no changes to use the fansite toolkit - and similarly, many of them likely won't see the need, and continue operating entirely on their own. Unless they are doing something seriously wrong, WotC isn't going to come after them.