Hello lone traveller from the future! In case anybody visits japan, buys the game and then encounters the same problems as I did, here is the solution to get everything running. Proton can't fix all of this, so you will ...
Additional information: The game was made by Gust and seems to - according to the window name - even use the launcher of Atelier Shallie, which is rated Platinum on ProtonDB with slight tinkering.