Right I agree with you. The reason i got the Onkyo is for extra HDMI connectivity (which i need for Apple TV, xbox, PC, etc) . My biggest beef with Samsung has been just 2 HDMI inputs. If not for that, I wouldn't have gotten the Onkyo. I really just want to switch the 'receiver hub' functionality from the Samsung to the Onkyo and keeping the Samsung as a BD unit with speakers.
I'm not sure how i'd test whether both HDMI outs can be active. When i outed one to TV and the other to Samsung, video was fine, but audio didn't work (perhaps audio should go in, not out).