I think there is some confusion on what rest level means for both 3.0 and 2.0. The "fresh" and "fairly fresh" text have absolutely no meaning other than labeling the % values you see next to them. It's just at some time we defined "fairly fresh" to mean 85%, but the real setting you are setting is that 85%.
Each player starts the game at 100%, or 100% of their peak, or 100% of their ratings. Basically when the engine uses their ratings, it is using their full rating. After each play, if the player was on the field, they will start to tire. This is represented as them losing this 100% and it will start to go down as they play. This percentage always represents the percentage of their ratings that are used in the engine, so if their fatigue drops to 90%, it means that their ratings will only be valued at 90% - a rating of 80 will now be 72 (90% of 80). This percentage fatigue has ALWAYS been in the game and those colors you see is just a visual representation of a fixed range of percentages. The "very tired" designation is just some percentage fatigue but it doesn't really mean the player is actually considered very tired in the engine. That's up for you to decide when you want a player to be considered "very tired".
The Rest Level is just saying that if a player drops to a certain percentage fatigue, you want them to rest and put someone else on the field. A higher Stamina player is going to drop in that % fatigue slower than a lower Stamina player. The rest level percentages has nothing to do directly with the amount of plays they are playing or on the bench. It just simply says once a player drops to a certain percentage fatigue, I want them to rest. As they rest, that percentage fatigue will recover and they will eventually no longer be considered resting and get back in the game.
If you are confused, just keep all the players at the basic default 85%.