Seems like you have the concepts down. Panorama is primarily about setting up the common settings that can be pushed to multiple devices via the groups. The general assumption is that specific site only settings are on the device. With version 7 and the template stack you could use a specific template as you suggest for each site. But I think that is going to make your Panorama interface very busy with a very long pull menu on 100 sites. Personally, I would stick with keeping the specific settings local and just changing the context to local in Panorama for maintenance. You are also correct that scripting will be your best bet to pre-load the configuration itself either on the device or via your Panorama specific device template.
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