It appears to me that when you run the ESRIRegAsm tool that it produces a file in the following directory:C:\Program Files\Common Files\ArcGIS\Desktop9.4\Configuration\CATIDThe name of the file is something like {GUID}_name.ecfg. The file itself is really a zip file which contains a file named config.xml. It appears that ArcMap is using this file to determine component categories versus that which is in the registry.
Thank you for the post, you bring up some good points. Unfortunately I don't have the answers to your questions at this time, but this information needs to be in the documentation for 9.4 final.I logged an enhancement request for you (NIM052616) to provide documentation on how to create and deploy components using ecfg files.
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