The refresh rate refers to how many pages you can flip in the *reader* before we trigger a flash.
The "Avoid mandatory black flashes in UI", on the other hand, applies to a whole bunch of UI interactions that *always* flash, regardless of where you are, (usually related to menu/pop-ups on show & dismiss). It's enabled by default to avoid ghosting, but it's available as an option because YMMV, and some devices deal with it better than others.
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