I applaud your effort to use a statistical analysis to understand our issues, but I believe your conclusion is flawed. % of minutes played does not translate into % of minutes available. What you're proving here is that the team isn't well constructed, that only a handful of players are nailed on starters, and that we rotate a lot - a point you concede when looking at Man City. You also mention that you can't speculate as to why a player wasn't picked and that you can't base it on club announced injuries, because that would be speculation not backed up by data. The problem with that, is that you presuppose that we have a best XI and that whenever available our "best" players will play. Which is also speculation, and arguably a more significant assumption.
Injuries are reported, and data is available to see how many matches a player actually misses because of injuries. The data supports that five players have been out injured for a significant amount of time. Allowing for one game "recovery" in the league per injury - 90 minutes matches not withstanding.
Tyrell Malacia - 0% available
Mason Mount - 21% available
Lisandro Martinez - 29.2% available
Luke Shaw - 37.5% available
Casemiro - 44.8% available
A number of players in your list have not been injured for nearly as much as suggested by their selections.
Garnacho - 100% available
Varane - 83% available
Hojlund - 70% available
Mainoo - 58.3%
Varane was left out of the squad for non-injury related reasons twice. There is an argument to be had as to whether the Casemiro, Martinez, Shaw trio is key to our entire team structure, but injury wise your XI actually looks like this - suspensions are ignored, because honestly that is self inflicted. 100% is indicated by no percentage added.
Onana
Dalot - Varane 83% - Martinez 29% - Shaw 37%
Casemiro 44% - Mainoo 58.3%
Garnacho - Bruno - Rashford
Hojlund 70
Now, not all of these players were significant last season, when we finished third, so it might be important to look at how much those players have been available this season - and our backups to key positions.
Scott McT 100%
Antony 91% - two matches special leave
Amrabat 87.5%
Eriksen 75%
Maguire 75%
Martial 66%
Which shows that there is primarily one position we've not had the personell to cover because of injuries - which is left back. The XI suggested in OP with second choice backups for long term injuries:
Onana
Dalot Varane Martinez/Maguire Shaw/Malacia
Casemiro/Amrabat Mainoo/Eriksen
Garnacho Bruno Rashford
Hojlund/Martial
A well built squad should be able to handle all but the left back issues. Recruitment has clearly been a problem, but at the same time there are players here that should be performing better on the basis of previous performances and ability (arguably a topic for another thread). Squad management is also an issue that could be, and probably should be, scrutinzed.