The Flash side was unexpectedly slow, and comments on this same article on Reddit indicate that it is because they are doing a lot of JavaScript-to-Flash communication, which is unusual for a game, as well as enabling "wmode=transparent", which allows DOM elements to be positioned on top of Flash content, slows down Flash content, and is apparently unnecessary for this page.
Flash defaults to "non-web-friendly" (windowed) flags by default, HTML5 defaults to "web-friendly" flags. As a commenter said, you can also make the canvas tag opaque by using a special browser-specific style.
If you remove the windowless flag from Flash, you would have to add the opaque flag to HTML5 to make it a fair comparison.
HTML5 allows you to position elements on top of the drawing canvas and use a transparent canvas so the background of the page would show through the drawing. Flash does not, unless you add wmode=transparent to the parameters.
I was wondering why the ball appeared clipped on the flash side, even though I can't remember having seen this problem in a flash game before. It was also unusually slow. That old 3D first-per-view demo with textures had a clearer image and was faster.