The day after I finished supporting the controller, I was horrified to find that when running on Steam, the controller controls were a mess, with all the various buttons messed up. After frantic research, I found that if you want to use the controller correctly, then you may need to adjust the Steam controller configuration!
First, right-click FREUS->Manage->Controller Configuration->Browse Configuration in the game library, and select the controller template, so that the controller can be used normally!
Luckily no one's playing the game now, otherwise I'll be scolded (a bit sad...ːsteamsadː)