I almost feel a little silly asking as I'm sure it'll make sense when I hit on the right example scenario, but why is it that Classic Netrunner used this scoring methodology:

"If you are keeping a running point total, you should play an even number of games, with you and your opponent trading Corporation and Runner roles after each game. The winner of each game gets a flat 10 points; the loser gets 1 point for each agenda point scored."

Aside from the benefit of tracking unconventional wins (e.g. flatlining the Runner), what mathematical benefit does this offer? Why not 7? 

I know Android: Netrunner seems to have dropped this, but that is irrespective of my point. 

Actually if you check the organised play rules on the FFG site they do use that system. I personally don't think it's a problem or that strange.

One point for each agenda, three points for winning. It matters because if the match goes to time in the second game, it gives an advantage in scoring prestige to the player who won the first game; this is pretty normal for games which are forced to have multi–game matches during each round of Swiss. Additionally, it matters because match points are the second tie–breaker when seeding for the elimination rounds.