

This game has a weird bug where you have to alt+tab for it to recognize the controller once you are in the actual game, not in the initial menu. This happens even on a Windows PC. For me to solve this on the Steam Deck was to simply open another app, Google Chrome in my case, then switch to it, then go back to the game and it should recognize the Steam Deck inputs now. You can close the other app to save some battery.

After the initial experience, when I went to play again I was unable to play the game; only menus responded. I tried changing controller configuration again, switching back to the one from the Developer, turning off Steam Input API, nothing. I could play the game once and since then it's borked.
I'll reach out to the Developer (if I can) and see if they respond, as I'm not the first and I doubt the last who will have this issue. If I post a 3rd review, it'll at least be good news... Clearly I spoke too soon after being excited to get the game working, and I did get some enjoyment out of it before it was booked again; that only rubbed more salt in the wound.

Changed basically everything.
30FPS
The official layout does not work outside of the main menu. Had to createy own layout emulating a keyboard.
That it appears that the Steam release has an official control layout and it doesn't work was frustrating. I lost a lot of time trying to get it to work. I ended up creating my own layout and that worked great; it's like the game doesn't support controller properly.
If you are playing, my community layout is "A Quintessential layout for study". Hope it gives you a better experience.

Make R2 as Left Mouse Click
During the Visual Novel parts of the game the default controller inputs would not work, changing to Gamepad with Joystick and having the Right Trackpad as Mouse and R2 set to Left Mouse Click made the game playable.
Even with the changed layout the next button isn't clickable, so you have to quickly press your Left Mouse Click button over Auto twice to act as next.