If I can just add my 2 cents worth here. I haven't played on BGA yet but I play on the app (I will start on BGA when I get more competent).
Is this possibly the faction board scoring versus the end game final score sheet? On the app next to your faction avatar there's a single running score. This shows everything that happens within the rounds and upon passing rounds etc. Then you have your end game score sheet which is the sum total of all of your scoring such as end game scoring objectives and from memory your research levels etc.
So the faction score is your running 'health' during the game essentially.