Since the VS Input Header descriptor only supports one bEndpointAddress I think you would have to present this as two VideoStreaming interfaces, i.e. bInCollection = 2 in the VC Interface Header descriptor.
So, you would provide one Output Terminal and two sets of Video Streaming descriptors.
Even with this, I don't think there's anything preventing the host from doing a probe/commit sequence on the second interface that conflicts with the settings required for the first - unless your interface is such that no configuration is allowed.
You might try these folks for a more definitive answer:
I did not get how you can handle two interfaces using same O/P terminal? If you had two streaming interfaces for one video source, how would you adjust video properties of both the sterams individually? Please excuse, if I did not understand your app well. I think 1O/P terminal must be mapped to 1 IISO interface. Can you please detail your app a bit more.