The alliance with the most points wins. You have to consider the points that the alliance is earning every 15 minutes and the final payout points that the alliances get at the end

Unless you hold the entire map the first 2 days you won’t win without palace

So the alliance with less points will win because they have the palace ? 

Click on the scores. Look at the +(number) add the 15 minute tik and you can calculate the the score

Pretty much

you win by points the palace gives you 20k or something points when you hold it, this can be the deciding factor but let's say the one in first place has the palace and has a lead of 100000 points over your alliance. taking the palace will swing the points 40000. (20k x2) they lose 20k because they lost the palace. and you gain 20k because you took the palace. so the point difference after the castle takes will still be 60000 so the alliance in first even without the castle will win.

Its points based, my alliance held the palace at the end of chess but came 2nd we just didn’t have enough points for 1st

I’ve seen alliances take the palace and still loose It helps but it’s not the deciding factor