IMO, a more opionate search would fix this. Just recommend the most active community and show the others in gray.
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Technically yes. The problem would be how to decide which community put in spotlight and which in grey (or any other meaningful distinction). Would it be automatic (if yes, how to decide the algorithm), or manual (if yes, how to decide how to left them). These things can be discussed out and solved, but we should be aware that these questions are here.
And it would work only for real duplicates of communities, not healthy separated communities based on actual, conscious and cherished differences.