Most penalties happens because of opponent's mistakes. Take Pogba's penalty against Spurs. If the Spurs player didn't pulled him down then that chance would have probably fizzle into nothing.
I fully agree with your third point. If Bruno was bought earlier + Pogba wasn't injury then we would have been more creative. However I believe that such a scenario would also impact our defensive stats.
Pogba forced a desperate defensive action due to good play. Mistakes/penalties happen when offensive actions force defenders to take a chance.
Occasionally, or if you are David Luiz all the time, it’s the defenders fault when no action was necessary or the situation is poorly judged. Even in those instances they only ever occur when there is a significant offensive action. Dier felt he had to track Pogba and challenge him as otherwise Pogba is free to pick a player in the box for a tap in. Saying penalties are all just mistakes is again being blind to nuance and shows a shocking level of ignorance of the ability to force mistakes through good play.
Now I’m glad you acknowledge the injuries playing a significant role in curtailing our offensive output. That was bound to happen when you have two box to box midfielders in our set up as most teams defend deep and you often need pure creators to deal with that either centrally or wide. We did not have the players to create consistently but that is not McTominay or Fred’s fault. They did not decide to allow United to be bereft or attacking depth.
Our average side due in no small part to injuries has statistically been:
De Gea
AWB Lindelof Maguire Shaw
McTominay Fred
James Pereira Rashford
Martial
With all due respect it’s not going to create chaos in the attacking third as there is no player in that side purely designed to pick out the forward movement.
Now if you improve the attacking prospects:
De Gea
AWB Lindelof Maguire Shaw
McTominay Pogba
Greenwood Bruno Rashford
Martial
You can see where the attack would go through. I think the benefit we would get from that (or Matic in place of McT) would far outweigh any defensive frailties that may be exposed.