@ssholloway: Because switching between cover and other modes is done at the same early point in time during boot when the hack starts, so you can't really do it at runtime with how it's designed right now (which is also why each 'mixed' mode feature request went unimplemented)
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You can trigger that part of the code slightly faster than a full reboot w/ the 'Restart X' button of the Fonts hacks, which restarts the whole graphics stack (lab126_gui), and not simply the framework.
EDIT: And to answer the second part of your message, because in cover mode, the linkss/screensavers folder is unused, it's not even looked at, the active file is hosted outside of the userstore.
Which technically means, that, at best, for one your usecase, you could tweak the KOReader startup script to setup a
single 'KOReader' screensaver, and switch back to the last cover on quit, but that's all.
Nothing much you can do about crappy covers, except fixing the files' metadata before putting them on the device
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