He knows how Bobby went, being blown away by two hitmen in a train store. Bobby never expected to see it coming, but he did and he felt those bullets too. Bobby wasn't dead when he was hit the first 4 or 5 times, he watched those two hitmen fire away at his body, he knew he was being killed, but he saw it.

Tony felt bad for Bobby, no one should have to go out that way. You're reading too much into it, Tony lives on, but we just don't get to watch.