This problem can be sorted out in a snap, if minute allocation were allowed. It doesn't even have to be exact minutes, a range would do as well. For example Starter -> 35-40, Bench Player -> 10-15. Etc. Substitutions could be made at default times during the game, when the starters get tired, or when the score allows it - to get to that target of the minute range. In a blowout the bench player would play more..
But of course this would make it easier to train players given the training system depends on minutes played. Which, btw, isn't exactly realistic either.