http://www.w3schools.com/html5/html5_video.asp

The HTML5 video tag natively supports multiple codecs, so all the IE team really did was implement that half correctly. They did not provide the WebM/VP8 technology from Microsoft.com for download.

<video width="320" height="240" controls="controls">
  <source src="movie.mp4" type="video/mp4" />
  <source src="movie.ogg" type="video/ogg" />
  Your browser does not support the video tag.
</video>

What they did is similar to what MPlayer did in Linux with the non-free packages where MPlayer was often bundled separately and the non-free packages containing proprietary codecs for ASF, Real, ect... sans license, were an extra download.

But here WebM is actively being used by Microsoft and WebM encoded videos are being officially provided by Microsoft Corporation on a Microsoft website.

Allowing multiple video codecs under HTML5, be it WebM or not, is not the same as providing the technology in whatever form.

So that's the difference. I am going to shoot an email to MPEG LA with a link to this post and see what they have to say about it.