Yep- It's in TB12's best interest to compartmentalize both internally and externally which it seems to be he is doing a great job of. I do think he has an appreciation and a respect for Bob's situation even though he may think he was a complete wuss in bending over to the NFL.
While no one really knows, I'm almost 99% sure TB12, Bob and Jonathan had a brutally honest discussion about this entire thing. While Bob did F up, I think he made it clear to Tom that his situation was highly undesirable one and he needed to do what he felt was in the best interest of the team and the league. In kind, Tom told Bob exactly what he needed to do and Bob/Jonathan told him that they would support him as best they could. In other words, they understand each other's plight.
At the end of the day, if ownership and GoAT have trust issues this whole thing falls apart. Thankfully, both sides were mature enough to realize that winning is the most important thing and find a path to closure that they can both live with.