Why are the reason to have the low score and low population bonuses?
Since the population counter on Cyrodiil is totally broken and people who want to PvP get stuck with tons of people just weanting todo farming in Imperial City. So you end up with almsot all of the population locked players in IC, and then a small group from the enemy can overrun the few players who actually PvP and ontop of this, they get the low population bonus, despite they are in majority outside IC.
So why do people inside IC count for population for Cyrodiil? because if if they didn't, you would get some proper number about how many from each side that is actually in Cyrodill and not inside IC farming.