Actually, I like using this strategy a lot when I train my big men in two positions.
Like in your example, in the first game I might have A, B as starters and C, D as backups. In the second game of the week I would then play with C, D as starters and A, B as backups.
After that, I end up having two players (let's say A and B) with little more than 48 minutes, and two players (C and D) with little less. To give some numbers, C might have played for 35 minutes and D for 25.
At this point, on Thursday, I let C and D play in the same role: the one with more minutes played will be the backup, the other one will start the game. In the example, D will only have to play for 23 mins and C for 13 mins. This is usually manageable, especially if you pick a very bad team for the scrimmage, so that you are sure that C will be on the court for the entire 4th quarter.
Of course, in this way, you still have one free role to let a fifth player play for 48 minutes in the SC.
The beauty of this strategy is that you never have to set foul trouble to "let them play" or substitutions to "strictly follow depth chart", you just let your coach do whatever he wants and ususally you're fine.