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I have noticed a bit that the top ranking comment will then contain a bunch of fragmented, semi-unrelated sub-conversations and the top comment almost becomes an OP of its own.

Yes, I noticed the same thing. Sometimes the first comments becomes so long, that it's almost impossible to reach the other comments - I even built a Chrome extension to be able to collapse them, but when the first comment is really too long it becomes difficult to manage anyway.

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