There would not be a 5 or 6 different Link combinations if you allowed the same character to appear in more than one rivalry.
At the most you have Ganondorf, Majora and Vaati, and the latter two would struggle to receive enough nominations IMO. Dark Link would make it if Bacon allowed it. Even then, if you were still worried, the combos can be put in the same division like GoTD (early Brawl/Melee, MM/WW, MGS Division) so that they don't wreck that much of the bracket.
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Tofa7 - LoZ-LoD | Hardcore
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