Adobe: Is there a definitive reference for both the video tag and the JS API used to communicate with it?
The HTML5 draft is extremely well defined (that's the point) albeit constantly evolving (hence draft).
Adobe: My assumption is that each browser provides a default set of controls. Can these be modified or do you need to start from scratch?
You can't modify the browser's implementation but you make your own with HTML5, or use one of many open source starting points.
Adobe: How do you do true streaming with the video tag (i.e. not progressive download)?
I don't think this is possible.
Adobe: Is it possible to provide some form of DRM protection for video in HTML 5?
No.
Adobe: Is there a tool that is optimal for encoding Ogg videos for Firefox?
Not sure.
Adobe: I remember reading that you can seek to any part of a video even if it hasn’t been downloaded yet. Is that true and if so, how is that achieved?
Not sure.
Adobe: Is there no hope for IE ever supporting the video tag?