That's why as I've said recently, it's best to start with balancing jobs against one another first, then designing the monsters.
Not only is it best, it's common sense. There will always be more enemies than characters being developed constantly. Balancing enemies first would require constant retuning of the jobs in response to unique enemies as they are developed. Kinda hard to grow attached to an iconic job if it's shapeshifting what it does constantly.
What I meant by variety of encounters is not too design one trick ponies or if you do. Look at the entire beastiary at the very least. What is the ratio of flying enemies to ground enemies? What jobs benefit most against ground or flying? If the ratio is skewed too far in one direction, balance the ratio. Magic versus physical weakness, balance it. Weak to Thunder vs weak to fire, balance it. Weak to piercing vs weak to blunt, balance it. Which enemies are player resource hogs versus which barely dent player resources, if players trend to a particular xp mob because it's easy on player resources and gives faster xp, balance it.
Use metrics and extend that into endgame content. In order to retain iconic job identites, some jobs will excel at certain roles. The only way around that is to try and mish mash jobs into shared roles. I say there is no problem with job uniqueness if enemies get balanced last and correctly.
I fear that SE is treading deadly water trying to balance jobs in PvE and PvP together. Either balance PvE and PvP separately or risk pissing off your PvP & PvE fanbase in one motion.