Depends where you think Rossi's "natural" finishing place in those two races was, I don't see anything other than two 4th placings myself, the corollary being he gained a net 3 points from his contretemps with MM at Sepang.
I guess it is possible Lorenzo might have finished 3rd at Valencia 2015 without MM's influence, but MM had been admonished by the stewards not to interfere with a contender in that race after the Sepang race, one of the odder instructions issued by RD over my time following the sport particularly given the finding by them that MM had committed no riding infraction at Sepang. So along those lines/making those assumptions regarding MM's influence gives Rossi the title by a one point margin, said margin due to MM passing Lorenzo on the last lap to win the PI 2015 race, a race he allegedly tanked..
Marquez's action in the Sepang race are so overblown. If you watch the race, Rossi attacks Marquez at the very next corner no matter where Marquez overtakes. It disrupts both of their rhythms, Rossi was just as guilty for the crime of racing as Marquez was. Without kicking Marquez off his bike there is no way Rossi comes third in that race. He should have been disqualified, but clearly wasn't so there was still a chance for Rossi to take the title. From a marketing stand point, Rossi wins from the back row, its incredible, even with everything against him, he still manages to win the title. All hail the GOAT etc. He loses the title, well it's not really his fault, he was cheated etc.
If Rossi gets 4th at Sepang and has no back of the grid start, he comes in the final round on 306 points to Lorenzo's 305 points. Lorenzo has to beat Rossi by one point at one of his strongest tracks. Rossi has to beat Lorenzo at a track he hadn't won at since 2004. That wasn't going to happen.
Watching the race from memory, the issue Marquez had, whether he wanted to pass Lorenzo or not was that the Honda couldn't get any drive out of the corners which meant he wasn't in a position to overtake Lorenzo. I am sure if it was a straight fight between him and Lorenzo he would have risked it to make a pass and get it to stick, but he had no such motivation, nor did he want to take Lorenzo out and hand Rossi the title.
What cost Rossi the title was that after getting a lot of luck and a lot of things go his way in 2015 was that as the season go towards the end he couldn't maintain his the results from earlier in the season that helped. Every championship requires some luck of things going your way that are out of your control. Any rider just needs to take advantage of that when they happen. For example, without Lorenzo's injuries in 2013 it is very debatable whether Marquez would have won the title that year.
Rossi had luck before the season even start with Honda ....... up their engine and/or chassis that resulted in both factory riders having struggles throughout the season.
Rossi had a dream run of circumstances in the first 3 rounds:
the inside of Lorenzo's helmet coming loose and affecting his vision at Qatar going a long way to causing him to finish 4th.
Marquez running off the track at Qatar causing him to finish 5th.
Pedrosa not starting rounds 2-4 at a time when being on a factory Honda or Yamaha almost guaranteed a top 4 finish.
Marquez choosing the wrong tyre in Argentina and/or the wrong strategy when Rossi was catching him.
Lorenzo wins the next 4 rounds but Rossi still has a decent amount of luck that helps him mitigate the damage:
Marquez crashed out in 2 of the next 4 races. From memory he was in front of Rossi but behind Lorenzo
Dovi has a mechanical at Mugello, when that was one of the few tracks Ducati could compete with factory Honda/Yamaha.
Pedro misses round 4, crashes in round 5 and is probably not at full fitness at the time.
Rossi got the win at Assen, it is debatable whether he should have been demoted from 2nd or not.
Without any luck involved really, Rossi got very strong results from rounds 9-12. The 5 races from round 8-12 where crucial in Rossi maintaining his advantage in the championship.
At Misano, both Rossi and Lorenzo engaged in a game of cat and mouse when it started raining at the second weather change. Lorenzo sat behind Rossi daring him to make the first move. Lorenzo made the first move and pitted first while Rossi had to do an extra lap on the wets losing time. Both had realistically missed the boat to challenge for the race win but whether purposefully or not, Rossi's decision to stay out there thus making Lorenzo stay out there for a lap or two longer than he should have ensured that if Lorenzo beat him h2h then he would lose a minimal amount of points. Lorenzo then crashed to help Rossi stretch his points lead to 23 points. If Lorenzo goes into Aragon 12 points down instead or 23, the title fight shapes up a lot different. Tactical brilliance from Rossi or a stroke of luck? Either way tactical blunder from Lorenzo.
Rossi only beats Lorenzo h2h once for the rest of the season. Marquez helps Rossi at Aragon by crashing out early, without the crash it is likely Rossi loses a further 3 points when demoted to 4th.
Rossi has a meltdown over PI and fails to realise Marquez, whether intentionally or not has done him a huge favour by beating Lorenzo. If Lorenzo has those extra 5 points he going into Valencia leading the championship, he isn't losing from there. Rossi removes any motivation Marquez had for taking risks to beat Lorenzo at Valencia or Malaysia.
This ended up way longer than I planned. I don't have much to do at work right now.
Interestingly I did just read a comment -
Giacomo Agostini told Italian sports newspaper La Gazzetta dello Sport that Rossi had fallen into Márquez's trap which led him to believe he was the more intelligent rider and that the reaction given to him by Márquez during the race was an expected one, "I'm convinced that Valentino was angry, exhausted and frustrated, but until that turn it had been a great fight. But Valentino was surprised. He is a great professional."
The exhausted part interests me the most. Clearly Rossi's move was out of desperation but I didn't think that it could have been because fatigue was setting in. I hadn't considered the fatigue factor, and Marquez believing or knowing that if it comes down to a duel between him and Rossi that he can outlast Rossi in the Malaysian heat.