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The new flash.display.Stage3D class works very similar to flash.media.StageVideo in how it behaves as a display object within AIR. Just like StageVideo, Stage3D is never added to the AIR DisplayList but rather exists separately from that stack of objects. As in the case of StageVideo usage, the DisplayList appears above Stage3D in the visual stacking order.
It’s important to note that Stage3D does not in any way deprecate or interfere with the “2.5D” capabilities introduced in AIR 2. Those APIs are used with objects added to the traditional DisplayList, while the new Stage3D APIs are entirely separated from that.
This will, no doubt remain one of the most deep and complex sets of classes that an ActionScript developer will come across for some years to come. Thankfully, Adobe has made the wise decision of providing early access of these new APIs to both rendering engine and tooling product creators.