The debuffs don't necessarily need to be attached to a particular job, just a particular role. If slashing and piercing resist down were in the shared role actions for melee dps, you could coordinate your loadout with your teammates to fit your comp, regardless of what it was. You could even implement it by letting the player choose between a set of mutually exclusive traits that add the desired effect into the job's existing rotation. I can see MNK's blunt resist down effect being difficult to implement this way, though, as there aren't really any other jobs that use the damage type.

They could do the same with the strength and intelligence debuffs for tanks, make them mutually exclusive, and force you to plan with your co-tank which debuff you're going to take in your loadout based on the fight design.

Procs will probably be tricky with PLD/DRK, but with both tanks potentially looking to have cover equivalents, I'm hoping that these skills will end up being used to fish for procs when you're not actively tanking. Another problem that hasn't been mentioned is the inclusion of Savage Blade in PLD's primary dps combo when offtanking, which can create trouble for swaps as well as DRK's knife's edge enmity lead. But if I had to pick one issue to resolve to make the comp more workable, it would be the slashing debuff issue.