Some code from the GitHub repo:

if (orderBy === "smart") { communties = communties.sort((a, b) => b.score - a.score);

The scoring algorithm: https://github.com/tgxn/lemmy-explorer/blob/main/crawler/src/crawl/output.js#L124

It says it takes away from it if you block instances. Seems like that should cause it to be lower.

      let score = 0;
      // having a linked instance gives you a point for each link
      if (linkedFederation[siteBaseUrl]) {
        score += linkedFederation[siteBaseUrl];
      }

      // each allowed instance gives you points
      if (allowedFederation[siteBaseUrl]) {
        score += allowedFederation[siteBaseUrl] * 2;
     }

      // each blocked instance takes away points
      if (blockedFederation[siteBaseUrl]) {
        score -= blockedFederation[siteBaseUrl] * 10;
      }

  // also score based subscribers
      score = score * community.counts.subscribers;

Looks like they just have tons of subscribers.

At the same time, I think it's gonna be a case of the most manipulative and spooky instance simply winning out because they aren't playing nice. Pretty easy to game the system with fake accounts, or lying about your own numbers.