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I would be fine either making them tied or ranking based on the amount of cash on hand. I'd probably poll the players if it looked like that condition might come up.

In the very unlikely, improbable case where two winning countries had the same number of sectors, I believe whoever has the larger bank should be on top. In the even less likely where both share identical banks down to the penny, then I say a poll or a tie or even allow the alliance leader to make that decision.

Well, in that case, one empire would have joined before the other...

Maybe they joined at the exact same time?  Then what?

maybe they are the same person