Personally I think the +/- stats need to be based of "100 vs. 100" or at ship cap whichever is lower.
In the case of things that have a cluster penalty, then at the "optimum number" of them (sentinel frigates: 2, electric bombers: 20).
For things that have a cluster bonus, tweak it so that the bonus is large enough to max out at 100 ships: you'll get the same relative falloff in power as they die, but not need 400 of them.
This will give you a baseline for how well the ships do against each other when in evenly matched numbers ("Ok, so 100 fighters pwn 100 bombers and have +90%, so to take out 1000 bombers, I should take 200* fighters").
*I'm not 100% on how to calculate M.A.D. but I think 200 fighters works out to killing about 1100 bombers at the indicated percentages before being all dead.