I just read Kokuhaku Kurabu and that's where this confusion began... What exactly is an "extra" chapter in a collection of oneshots? I mean, an extra usually is a oneshot that has little or nothing to do with the main story... But when there is no connection between chapters anyways, then why is there a so-called "extra" chapter/story?

~4400 manga completed
~1700 ongoing...

Dont know how it is in your example but an extra can be an extra released in the volume only which might not have been published in a magazine before (or something like that)...

Because it is somehow different from the regular chapters, even if they're all standalone stories. For example, if regular chapters are numbered, the extra wouldn't have a number. It can be different in size. Or it can be a 4-koma. In a volume, extra chapters are clearly differentiated from regular chapters.

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Extra chapters are released outside of schedule, usually released with the volume release as a bonus to get readers to buy the book or at othertimes to advertise the series or just because.