I did the changes in ebrmain as described in the OP, which then did enable the "Network Libraries".
To test the syncing to /var/run/device.cfg I then changed the /mnt/secure/device.cfg and /mnt/secure/device.cfg.back to have "have_opds=0". Rebooted.
After reboot /var/run/device.cfg now also has "have_opds=0" but "Network Libraries" still enabled...
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