At some points Tom is about this close to being asked to shine the shoes of Neri and Rocco.

Ok, maybe exaggeration but I think that Michael's relationship with Tom, and increasingly with everyone, was purely transactional, not functional. It was the biggest difference between Michael and Vito and why even though both men were, for lack of a better word, evil, we see Michael's decay and fall as tragic.
That little speech Michael gave Tom before leaving was certainly designed to play to Tom's weak points because at that point in time, Michael had no choice but to trust him. It wasn't out of love but cold calculation. I don't think Michael believed anything he said about brotherhood with Tom. The gratuitously cold way he treated Tom upon his return was I think, his true feeling towards Tom.