I dont think you can do what you need. For my game, I needed to display ads via Appnext, but as you mentioned, unity3d renders ON TOP OF EVERYTHING, no matter what in the canvas page.
So, as a solution, I injected some javascript code in my canvas page, and whenever I wanted to show an ad, I would call the javascript function that made the canvas of the game 1px x 1px, show the ad, and when the ad was closed/clicked, restore the size of the game.
Hope this helps