KOReader starts in the native orientation for that device. That usually matches the logo when the device is booting, but that isn't required.
From that hw rota you have: CW (clockwise), Original, CCW (counter clockwise), 180º inverted.
If you don't get these values when you press the relevant buttons in the UI then I'm afraid your device(s) doesn't follow the specs (maybe the screen was mounted upside down?).
All of this can be fixed but you'll need to specify the rotations you'll get when you press the buttons and the hw device id, to let the program know your device uses an alternate way of rotating the screen.
More context and a way to start the app in fullsensor mode is in
https://www.mobileread.com/forums/sh...&postcount=350.
Keep in mind we need to fix the specific rotations to match what the UI expects before you can enable the "follow-the-sensor" mode.
About settings/preferences. They're indeed for each book. A long press on a setting would prompt you to apply that setting by default. It does that for new books but already opened books will keep their own settings.