1. The differences between MCU and the comics are broad enough that I'd be willing to take them as two different canons. That tends to be case by case depending on the adaption.

2. If there is in game footage I can't see a reason why a PB would be necessary, especially when it's a modern game with pretty good graphics from my understanding.

3. I am very unfamiliar with Doctor Who, so you may have to clarify what you mean by this question. Any character can potentially be canon updated, and canon point is your decision.