Yes, I supplied some code a while ago to have the content server to serve kepubs with the ".kepub.epub" extension. That was needed for them to be downloaded by the browser. But, I didn't think about the metadata update issue. At the time, this plugin didn't exist (well, I might have had a version), so calibre couldn't have done it.
I suppose what this needs is for the server to handle any format that calibre has a metadata writer plugin for. And the plugboards to recognise this as well. Kovid is in the process of rewriting the content server, but, apart from seeing lots of code updates, I haven't looked at it. Hopefully, the changes will include handling non-standard formats, but, I don't know. I'll try and have a look.
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