I think you failed to convey that clearly. I certainly misunderstood.
Let's try to redo the 1550 expensive fighter vs a single BB again. I have to start from scratch:
Fire at a BB:
Barbette: 2D +7[basic] +2[small vs ship] -7[targets basic defence] = 2D + 2 ≈ 9 => 80%
Barbette: 3100 * ( 80%[hit] - 45%[armour] ) = 3100 * 35% ≈ 1085 damage killing ~12,3% of the BB every round.
BB fire at fighters:
ToHit (Close Range): Basic attack: +2[crew] + 3[FireControl] + 2[TL] = +7.
Spinal: Can't attack fighters (<2000dT).
Large bay: 2D +7[basic] +1[accurate] -6[targets basic defence] - 2[small] = 2D + 0 ≈ 7 => 50%
Medium Bay: 2D +7[basic] -6[targets basic defence] - 2[small] = 2D - 1 ≈ 6 => 35%
Small Bay: 2D +7[basic] -6[targets basic defence] - 2[small] = 2D - 1 ≈ 6 => 35%
Barbette: 2D +7[basic] -6[targets basic defence] = 2D + 1 ≈ 8 => 60%
Turret: 2D +7[basic] +1[accurate] -6[targets basic defence] = 2D + 2 ≈ 9 => 80%
Damage:
Large Bay: 42 * (50% - 45%) ≈ 2
Medium Bay: 620 * (35% - 45%) ≈ 0
Small Bay: 620 * (35% - 45%) ≈ 0
Barbette: 580 * (60% - 45%) ≈ 87
Turret: 882 * (80% - 45%) ≈ 309
2 + 0 + 0 + 0 + 87 + 309 = 398 Damage killing ~18,3% of the fighters. BB win.
This makes no sense whatsoever, none of the BB's weapons have any trouble penetrating armour. If they hit they will penetrate and do damage, e.g. the medium bays are ortillery doing 2DD ≈ 70 damage, Armour 15 is hardly noticed, yet now they are completely stopped by that same armour.