I wouldn't be surprised if Black Widow's father turned out to be Taskmaster. Marvel Studios had certainly shown that example in GOTG 2, regarding Star-Lord's true father. Not everything will be like the comics.
Endgame showed that there are alternate realities, where events can happen differently. In this case, the writers don't have to integrate the mutant race into the main MCU timeline. In one of the alternate timelines, the mutants have existed alongside with the Avengers. Therefore, mutants are still part of the MCU, but they don't exist in the main MCU timeline.
So, no. It's not too late for MCU to portray Magneto as a holocaust survivor.
2. Thor was out of shape because he lost his Asgardian family and failed to prevent Thanos from decimating half of the universe. What's worse? He beheaded Thanos, which none of the other Avengers could have done. Besides, Thanos was already weak after using the Infinity Gauntlet.
3. Loki must have escaped to another timeline. This will be explained in his solo series.
4. Iron Man started in 2008, which jump started the rest of the MCU. So, it makes sense why he had to die in Endgame.
5. Everyone has their own opinions about the movie. Some will like it, some don't. I enjoyed the movie, despite the fact it was three-hours long. But the one thing that scratches my head is time travel.