It's not unrealistic to assume Massa suffered the same tire prblems Shu had. And it has to be noticed that once Alonso did get past him, he never really got up to the pace he enjoyed at the beginning. Trust me, he wanted 3rd very bad, but couldn't do it. If Massa really was running interference and trying t back Alonso up, I don't have a problem with that, it's racing. It's Alonso's problem he qualified so poorly, and his problem if he couldn't pass Massa.
I would consider myself a naive fool if I believed teams did not have secret ways if signalling drivers There are so many easy ways to do this. As well, all teams go through a pre-race briefing, and just like a soccer game, the drivers are briefed on what the team expects them to do in certain scenarios.
This isn't the first time Ferrari has won with strategy, they really know when to play their cards. This kind of struff makes the race for the title more exciting.