When no one answers your first question, it usually means no one knows.
MC uses DLNA, which sees DLNA Renderers. I don't know if MC sees the UUID for DLNA commands or not, but it would seem logical that it sees the IP Address of the device and responses to DLNA and SSDP packets. I think if you want to control the Yamaha Zones from within MC, the Yamaha needs to present two DLNA Renderers. However, you did say;
The app treats the Yamaha Zones as separate renderers.
So
maybe you could send commands to the Yamaha to switch zones using an appropriately composed URL, perhaps from a menu in Theatre View since Standard View doesn't have the capability to add a menu item that could send URLs, although maybe a Send To command, or maybe...? Then MC should see one zone disappear and the other zone appear. You could also just use the Yamaha App to switch zones on the RX A1080, wait for MC to find the new DLNA Renderer, and then play to the new Renderer. You just won't be able to see both zones at once, unless the RX A1080 presents both at once. It sounds like it doesn't, except to the Yamaha App.
If you use the Yamaha App to switch zones does MC see the new DLNA Renderer?
I think this is more a question for Yamaha than JRiver.