The way it works (as far as I can see) is that you can control scenes that are stored in scene enabled devices; however, you can create scenes in TE that control non-scene enabled devices. For example, I can set up a scene that dims the lights in the living room, turns on the lights in my garden, and turns on the lights on the front porch. The front porch switch may be scene enabled, but the garden lights and living room switches are not. In this case, the parameters for the scene is stored in the TE database and are not available to ZWave commander. If Zwave commander executed the scene only the front porch would respond as it stores its scene data.
What I understand that the ZWave Commander developer is asking is that an API be provided to allow him to read the scene information in the TE database so that he can get to the scene data and then send the appropriate commands to the relevant modules. I can't say that I know the ZWave protocol or TE apis, but I cant imagine that this would be too hard to do.
Why don't the ControlThink folks network enable TE and provide a REST/Webservices API to the product. That way it would be easy to develop apps against TE without having to write a Windows server (like ZWave Commander had to) as well as still have TE running at the same time. This would allow 3rd parties to develop apps for the iPhone/iTouch/Pre/Blackberry/Nokia phones and any many others.
I believe the author of ZWave Commander has offered to donate the code to ControlThink, maybe they should look into taking him up on it