Well, you have a point in that Tony's thoughts about various situations seem to be unclear. However, in the end, all things work out a lot better than expected. It cannot be pure luck. It may be that Tony is accustomed to thinking about things in a certain way before he takes action.

Season 4: Ralph does anything he can to cause trouble and Tony wants to kill him. His crew doesn't like even Tony's beating of Ralph and so Tony has to wait. When Johnny Sack hears about the Ginny joke, Tony can dispose of Ralph without him even getting involved. Instead he chooses "not to give up his captain". Eventually he does it himself in such a way that no one can be blamed for sure.

Season 5: Although Tony B has already done a job for Carmine Jr without Tony's approval, Tony does not admit that, with the danger of being directly involved into the war between Johnny Sack and Carmine Jr. In the meantime, he favors Tony B over other members of the crew and especially Chris. When Tony B kills Leotardo's brother, he refuses to hand him to Johnny Sack, bringing more heat to his crew who protest all the time. Again, he takes care of the matter himself without having to be pushed around by the NY crew.

Do you see a pattern? I see one. Tony likes to push situations to extremes in order to assess everybody's reactions and to gather useful information to be used later. In the end, he does the obvious thing and emerges as the one that is in complete control of the situation.

After all, we all have seen people in real life who, despite the fact that their thoughts and actions seem totally incoherent, get exactly what they want in the end.