Not sure about your first question. (May be possible with a user patch, but not in the UI settings.)
Regarding the folder access: strangely, I also can't navigate to my Android home folder /storage/emulated/0/ on my phone if it starts in the system directory. However, as a workaround (if you haven't done so already, anyway), when you're in the File browser looking at your book files, set that folder as your Home folder (Plus button, Set as HOME folder). Then, when you want to set your custom cover, tap the Home symbol to go to your book folder, and from there you should be able to navigate to your other freely accessible folders on your device.
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