Thanks for playing and providing feedback!
Well, actually there is no need in third slot of automation. As you progress in game and unlock new content, you get alternative ways of getting resources. Maybe will add a third automation slot in the future, when player unlocks new actions and resources. Regarding rest always automated - you will pretty soon unlock research (that persists through resets) that would make rest almost useless. As you prestige and invest in green banners, you will also get pretty high multiplier to physical training, that will dramatically increase energy income. Energy is a bottleneck only at very early stages of the game.
I'm at the point where I wish tier3 of banners was already accessable and all of my researches cost at least 2k to upgrade and I still want more automation slots lol.
It's not about rest being actually useful or not, having rest be automated from the start would make the grinding after a prestige a lot easier. In the end it's your game and so the balance is up to you, I just think it would be extremely convenient.