I say B, with one tiny adjustment.
Modified loss needs to be 0 points. Otherwise, the players can fabricate an ID by figuring out what they need to destroy from each other and then wait for time to both secure at least 1 point.
That's my thinking, too.
But I really like the idea of extra points for tabling someone.
Full Win (lost no ships & destroyed all opponent 's ships): 3 points
Standard Win: 2 points
Modified Win (by less than 12 points): 1 point
Loss: 0 points
I think this would solve the ID problem and also make later rounds more exciting as you could jump up the table with a full win. Although I guess it would work against swarms...
Vs