These are all excellent observations. The variety of them shows just how much nuance is contained in that brief scene. I'd like to add a few:

I'm usually far more sympathetic to Tom than to Michael. But, in this case I think Michael was legitimately pissed at Tom for several reasons. Michael was stunned and dismayed when he learned--after he testified--that Pentanageli was alive. Tom's reply was insulting: "Roth, he played this one beautifully...you've opened yourself to five counts of perjury." Tom was praising Roth and chiding Michael. Not very "brotherly."

Tom over-reacted to Michael's order to kill Roth ("It'd be like killing the President...do you have to kill everyone?"). That type of lawyerly over-caution might have been necessary for Sonny, given his hot temper, but not for Michael, who'd correctly thought it through and concluded that Roth was his most resourceful and dangerous enemy, and had to go.

Tom had also had let Michael down badly by screwing up. "Our people with the NY detectives said [Pentangeli] was half deadI, scared.talking out loud about how you betrayed him..." If Tom did his job right as Michael's liaison with the NY detectives , why didn't he pick up that Pentangeli survived before Michael testified? And, when Michael asked, "What abot Fredo?", Tom, who was Michael's liaison to Fredo replied, "He says he knows nothing--and I believe him." But, Fredo knew Pentangeli had survived--and, more important, that the Senate lawyer, Questadt, "belongs to Roth." Why didn't Tom get that out of Fredo before Michael testified?

Michael needed Tom for two critical missions at that point: To persuade Vincenzo to come to America to show himself when Pentangeli testified, and to persuade Pentangeli to kill himself. He had accumulated doubts about Tom's attitude toward him and his judgment, That's why he got tough and hurtful when he asked, "Are you going to come along with me in these things I have to do?"

When Michael says to Tom: "...you can take your wife, your family and your mistress to Vegas..." the camera pans to Neri, whose smug, self-satisfied expression tells me that he was the source of that tidbit.