After the suggestion from GM-Manon here
(268489.16) and EGM-Perpete here
(268489.19), I've decided to open my first topic on this bug (or Game Manual error). So here is what the Game Manual says:
Substitution Pattern
The coach will sometimes use his own judgment to decide what the proper balance is between starters, backups, reserves, and even players on the bench but not in the depth chart at all. You can set the balance between how much coaches use their own judgment or defer to yours with the substitutions box. You can use entirely your judgment (Strictly Follow Depth Chart), entirely the coach's judgment (Let Coach Decide), a mix between the two (Coach Picks from Depth Chart), or you can use your depth chart strictly until the 4th quarter, then tell the coach to try and win the game however he thinks is best (Depth Chart until 4th).
There have been multiple issues in the current GE where, after selecting "Strictly Follow Depth Chart", the coach is allowed to defy the orders issued by the manager and substitute players (who are still able to play) with others who are not set in the depth chart.
In other words, in Strictly Follow Depth Chart, the coach may decide to NOT follow your judgment.
Now, since this is completely different from what the Game Manual says, it must be a bug or the Game Manual is inaccurate/wrong. If everything is working as intended, I urge the developers to amend the Game Manual to reflect that there is no option in which the coach follows entirely the manager's judgment. If it is not working as intended, I urge the developers to come out, say so and elaborate a plan and schedule for a fix, exactly as it has been done for the Blank Line-ups issue.
This inconsistency has been around forever, just as Blanks did. It is time we have a clear answer on it and the Game Manual is amended, if it needs to.