The reason for embedding jetty into the app versus starting it manually is ease of maintenance, for one. I don't want to add the complexity of a customer having to stop, start and manage a web/app server. Embedding Jetty allows my application, not a sys admin, to control the servlet container.
I'm still not sure what you are trying to achieve with using an embedded jetty instance over a regular one. I've never used an embedded jetty instance, I just start jetty as a regular servlet container and deploy my applications as war files (although you can, as we discovered earlier, use an exploded dir structure). It just happens that some of my applications don't produce html. They expose services instead (although I have one that does both).
I have exactly what you want. Multiple rich clients accessing networked datasources (eg database, web services, etc.) via a service layer exposed via HttpInvoker. If i want to change servers I just change the serviceURL. So I still don't see what the embedded instance gains you, and it's causing you a lot of problems. Can't you just use a jetty as a standalone server and deploy your services as normal then access those services from the client?