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Discarding 50% of the results is simply excessive. What's the point of having multiple stages and the organizer putting in so much effort? It's easier to run just one tournament and not overexert oneself.
It would be acceptable to discard one or two results, depending on the number of stages, but in any case, keeping less than 75% of the results undermines the very essence of a multi-stage tournament.
And determining the winner based on their overall ranking seems like the simplest and fairest approach.
However, there's an opinion that the difference in results (days) won't be taken into account. But in that case, it's necessary to choose one or consider both of these aspects.