Thanks for the replies, unfortunately I saw the last one too late.
It seems to be exactly this issue, since I just had another motor short out. At least now I know what caused it, because it was driving me insane. The replacement motor printed for a couple of days without any issue though so at first I thought I had a rare faulty stepper. But it seems it most definitely has to do with this bug. Both three steppers burned out exactly as written in the description, feel really bad that 3 stepper motors got burned out this way before finding out the cause.
There should be a warning about this very thing in the Klipper Duet example files. Or at least somewhere that a Duet user will see.
The best solution/hack to solve this issue with Klipper is to disable the 5V line it seems.