Whereas every job is affected by it, They are not all affected in the same way. For some jobs it is a benefit. It holds back the strong melee jobs by giving them less value for their gear and job abilities. this allows weaker melee jobs to catch up.

Also as u stated 999 is not the cap. 999 has nothing to do with anything. The difference between your attack and the monsters defense is the important thing here.

And having a bigger window because of higher base weapon damage doesnt change much. Base stats and strong bonuses on gear outside abyssea. Prospector buffs and atmas inside abyssea.