In Alliance war, you earn points by attacking a team and ending the fight with the defense having fewer hit points than when you started the fight (with rounding considered). An entire alliance is worth about 1500points (give or take a few) divided among all the members based on hit points. This creates some weird interactions where two of the exact same team on opposing sides are worth different points.
How about an example?
Great idea! Let's say each side has 3 members (pairings always have the same number of participants, with the exception of if a member doesn't field a team).
Team 1 hps:
A:4000, B:3000, C:2000
Team 2 hps:
D:5000, E:4000, F, 3000
Yes, Team 2 is more powerful than Team 1. Pairings are rarely even. In this case, B and F have the same hit points, but since B has 3000/9000 hit points, it will likely get 500 points, while F will likely have about 375 points because it has 3000/12000 hit points.
So if I remove half of the hit points, I get half the points?
Not exactly. The points for a single team are 2/3 for doing damage and 1/3 for the kill. So if a team is worth 300 points and has 2000 hit points, if you deal 1000 damage, you'll get 100 points. Then if you use another flag to finish them off, you'll get 200 points for that last 1000 damage.
It's also important to note that there can be weird rounding situations, so if you kill a team in one hit, you'll get 300 points, but if you take two hits, you'll get 301 points.
I hope this clears things up!