substituting my starters for bench players when there is 5 minutes left to go in a very close game
You didn't mention anything about fouls. Perhaps they were in foul trouble?
They didn't even have 30 minutes, so they couldn't be very tired
It isn't about how long they have played the whole game but how long they have been on the court at a time. A player can have atrocious stamina but it isn't about him not being tired cause he only played 30 minutes but more about him getting tired when he only played 15 minutes, needed to take a rest and then come back in for another 15 min and is now tired again. So stamina could still play a part in it.
Playing Strictly follow depth chart means your players get very tired in the end as the starters play most of the game. So maybe the coach decide that the backup will play better than the starter at the end of the game due to stamina issues.
Let coach decide will give full control over to your coach. Generally most teams don't use it cause it can give a lot of wtf results/substitution patterns as the coach will make substitutions in what he deems fit and might not be what the manager deems fit. Never ideal for training purposes
Depth chart until 4th will follow your designated depth chart until the 4th. In the 4th, the coach will decide. So unless you fully trust your coach to make all the right decisions (which I don't), then I wouldn't use it especially with the game on the line.
Have you considered Coach picks from depth chart? It is the compromise between giving complete freedom to your coach and you having control over the substitution pattern. Basically a player will be subbed out whenever the coach believes the backup will play better than the starter based on stamina.
You will need to experiment to see which one works for you.