There are several ways around this. As you already mentioned, you can make separate assemblies in Visual Studio or create your own deployments using Mage / MageUI, however, if you need one set of deployment files but for the application to be recreated based on some other details, the best way is it's likely to play around with the idea of virtualizing or configuring some deployment files on the fly, exposing them through the ASP.NET user website. I did this successfully using VirtualPathProvider, but you can probably use a custom handler.
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