Among other things, Nightmode build 13 lets you set a separate page-refresh value for when you're in night mode versus day mode; with the firmware version, you have to manually adjust page refresh, if you find you need a more frequent one in night mode, each time you invert the screen.
Also, toggling the firmware version requires a deep dive down several layers of menus for which you must exit the book you're reading (unless you also use NickelMenu); whereas Nightmode patch lets you set a trigger level of brightness (I toggle between day and night at 100% brightness) or control it with a user-adjustable long press of the physical light button, if your device has one.
In short: Nightmode is easier to use and is much more user-configurable; the firmware version is a bare-bones implementation.
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