I'm not a Mercedes fan at all, Mercedes is my archenemy but FIA stole the title from Hamilton.
Yes, it is quite clear. They broke two rules in order to ensure Max won. If they'd only broken one rule, either a) all lapped cars overtake, instead of some, or b) safety car goes in at the end of the following lap, not immediately... then there wouldn't have been time to resume, and the race would have finished under safety car. The only way they could get Max to win was to break both rules and also keep everyone out on track. In fact initially they said lapped cars
could not overtake... but then realised (perhaps under pressure from Horner on the radio) that if they did that, then Max wouldn't catch Lewis. They not only broke both rules, they also went back on a decision they'd just made.
And the reason about "we wanted to let them race" rings hollow... if they wanted that, then red flag it as they have done in the very recent past, let everyone get new tyres on, and then have a few laps of honest racing. It's quite clear that what they actually wanted was a new champion, to try to get some new interest in the sport, because it's boring if the same person and same team wins every year. Engineering a situation where you have one driver on fresh softs and another on very old hards, and saying we will let them battle it out is utterly ludicrous to anyone with even a basic knowledge of the sport... no way in hell Lewis could hold off Max for a lap in that situation.
the Race Director [...] could ignore the rules and make up a new decision on the spot. Which means that we are talking about Masi being able to let only 5 cars overtake the safety car and keep others behind, that is literally against the rules in the handbook but at the same rule book it states Masi can do whatever he wants.
Yes. Mercedes may or may not appeal, but it's not likely the result will be changed now. It's not a great look for the sport. Many people will not recognise Max as the champion, and even in the very unlikely event that the decision was reversed, many would not recognise Lewis as champion now either.
Personally I would welcome a new champion after so many years of Hamilton winning every time... but I just can't see Max as the world champion, because he didn't win the title, it was taken from the actual winner and given to him just to create some interest. So we have this weird limbo now.
Edit: I've just been reminded of this, too:
In 2020, there was a safety-car period during the Eifel Grand Prix at the Nurburgring. Both Hamilton and Verstappen complained it had been unnecessarily long.
Masi was asked about this after the race. He said: "There's a requirement in the sporting regulations to wave all the lapped cars past."