The idea of crafting bonuses on weapons is just a bad idea...

Have you really considered what you are saying:

To illustrate lets take an T-5 escort:

Fore Weapons

Lets just craft:

DHC [DMGX3]; DHC [DMGX3]; DHC [DMGX3], Quantum Torp [ACC X3]

Rare:

Turret [DMGx3], Turret [DMGx3], Turret [DMGx3]

See the problem ...