His after race quotes indicate that they missed the bike set-up by some amount. I believe that he played a very smart race, stayed in it for the championship points. At this point it's the season that matters, not the specific event. I'm sure that he is strongly incentivized to win races and even more so to win the championship. Pushing too hard on a bad set-up could lead to a crash and an injury, which is about the only thing that can keep him from winning the championship this year.
Even if they ran out of engines and he had to start from the pit lane at the last race he would still have a significant points buffer. He could completely miss the next three races and still hold the championship lead. That's astonishing considering there are only 7 rounds left in the season.
It's clear that some of the other teams and riders have found additional pace in the second half of the season. The finishes are getting closer and there is competition for MM93 later in the race.
It's racing, and anything can happen, but I don't see anyone in a position to seriously challenge Marc for the championship win this year.