User blog comment:Kaido King of the Beasts/Cover Mini-Review: Solo Journey of Jinbe, Knight of the Sea/@comment-3075024-20150519212444/@comment-10543621-20150521015756

It really depends on how you define 'affects the plot'. Every cover story so far has had a foreshadowing effect or has been carried out into the main storyline, usually in the form of past characters reappearing. Thus it stands to reason to expect other characters featured in cover stories to eventually reappear even if they haven't at this point. Eg being Enel, CP9, Gedatsu (although who really cares about him?).And usually, past characters reappearing tends to be the biggest effect cover stories end up having. Jinbe is the same here.

However, the fact remains that for someone who doesn't read cover stories, they're essentially not meant to miss much in terms of overall plot progression. The cover stories usually feature details that DON'T affect the main plot, while ending with a main reason for the story which will affect the main plot.

So yeah, they affect the main plot, but you really can go without paying them any attention if you don't want to.