I just found out that I am not the only one who thinks the IBJJF way of calculating team points is weird. First of all, the belt level should have some bearing, because at least in my opinion winning a white belt division means very little when comparing with winning a brown belt division. At least if the brown belt division has a reasonable amount of competitors. I think you should also win at least one match to receive any points from third place etc.
Another important measure to look at is actually points per number of athletes. Potentially this could also be weighted according to belt level..
Transworld jiu jitsu article