But it could and it's not fair, that in that particular circumstance BRD/MCH would be at a disadvantage. Completely game-breaking balance. (end sarcasm)
You are pretty much dead on with that. By looking at a lot of battle logs comparing BRD/MCH in the cases where BRD has a higher advantage it would most definitely be offset by the Bishop Turret offering an increase to Melee damage as well, as well with the Rook Turret being able to transfer the debuff to multiple separate mobs having a "General" debuff through hypercharge would definitely be the best approach to balance.
Where does this keep coming from? That because BRD/MCH has lower weapon damage therefore they have lower damage?
Do Melee have lower damage than magic users because Magic Damage is higher than Physical Damage? It's just a method to control damage scaling with gear and based on the job play style. If BRD/MCH Physical Damage matched Melee Physical Damage then they would put out so much more damage than Melee could and would almost match SMN in AOE potential.