I'll compare it with the game he most heavily rips off, Hitman. Specifically Hitman 2016.Many games implement tutorials as a hint system, but they always try to pop up a message before the player does something, not after.
I don't know if it will work in YS though. Tons of YS mechanics are finicky Rube-Goldberg machines and you need to properly learn them to be able to utilize them correctly. Going into the game blindly without spoilers will always lead to failure.
For example, consider this kind of message: "You picked up a katana! To attack, press E." In RPGs or action-adventure games, this is usually all you need to know. In YS, using a katana forces the player to commence a complicated procedure of destroying all the evidence and potentially also eliminating the witnesses. So either you need to expand the original message to explain the consequences before the player kills someone, but that becomes spoilers and also TL;DR, or you can add an additional message after murder: "It seems people bleed when stabbed. New tasks: 1. Find a mop to clean up the blood. 2. Dispose of the body." In fact, a checklist-driven tutorial would be the optimal solution given this game's situation, but would obviously lead to what you said: player learning about a fuckup after the fact.
Based of the latest Jay's video, auto-attack happens only if you have your weapon out. If you hide your weapon, you can try restoring your sanity by laughing or stalking senpai.
Murder for hire is a complex process that takes many stages, so how does Hitman handle it? They set their tutorial during the actual training/final examination of the titular Hitman by the shadowy organization that employs him.
All tutorials take place in a pretend enviornment, re-enacting previous hits the agency in question had carried out. All the people and victims are employees of the agency, and the buildings are elaborate mock ups made of plywood and other basic materials, giving a thematic reason for handholding that gives flavor to the entire level.
The first mission is entirely handheld step by step. Teaching you the basics of murder, disguises, disposing of bodies, staying undetected etc. The second mission is the exact same mission as the first one, but this time you have the freedom to try things yourself. The third and final training mission is a large scale level that is different from the first one, with multiple long winded methods to accomplish your goals, and in a way, despite still being set in a training environment, forms the first level of the game proper.
The intent is to slowly ease new players into the game, while keeping it from getting boring for returning players. Now compare that to "you fucked up" pop up boxes.