Certainly having multiple AOS servers is another plus factor in getting issues with development and deployments. I would however mention that you should not be doing development in a multi AOS topology, because of the exact same cause you mention: VS connected to one AOS, SSRS configured to work with another can cause issues. I would suggest you try to develop in a one AOS environment and then move the TEST to a multi AOS scenario. Plus, when you are doing deployment in a multi AOS scenario, for instance the Full CIL should be done on one server with the rest being closed, and then restart them sequentially. I'm not saying this applies to SSRS deployment, but the deployment relies heavily on the system wcf services, so, I can see some interference.
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