This is ultimately a lack of flexibility in the current framework. There's a couple things to consider.
A) You cannot use a "Tax when Used" paradigm and then equalize the damage component, because then you move into functional obsolescence. Why bring the job that does 10k DPS when the other jobs also do 10k DPS but bring all the goodies? This is a case of it's better to have them than not.
B) The inconsistent valuing of non-damage utility. How much is this particular bit of non-DPS oriented goodie worth? Opinions will vary widely. The perspective one has on what's more important will change that value.
C) The tight tuning of the encounters. Even when overgearing the encounters, current content cannot be completely ignored. This is how they design. Within this relatively tight windows where all the numbers fall, the game's scaling doesn't allow (and arguably shouldn't allow) players to start a tier clearing it at 50% potential and then capping off at 100% potential (killing the boss at 50% of the enrage).
Within this limited framework, even basic solutions are problematic as they cause problems down the line. There's only so many times we can add 10 potency.
The first step then is that the framework has to change. The Role system first has to expand to accommodate the growing number of jobs. And as a disclaimer, this is less a solution, and more a process to lead to a hopefully more desirable gamestate.
1a. Formalize the Flex Spot into a role, and shove the problem children into it. The "Problem children" being Black Mage, Samurai, Machinist. One can argue that potentially one more melee fits there, but that's a different discussion.
1b. Those in this role gain a trait that increases the potency of debuffs on the enemy/buffs on them from other roles. This is, in effect, their "RDPS" contribution, and the safeguard / tuning lever against being ignored in the future, as well as ensuring that bringing two of them is undesirable.
2. Equalize the baseline "DPS" values of the now 4 DPS roles. Everyone does ~10k DPS by themselves outside of a party. (For example).
3. Role action rebalance. Actions that crossover into other sides of the Trinity (Tank/healer) should have their power reconsidered. Specific example - Caster raise being made into an emergency raise with a long CD. Healer Raise is given a free "Swiftcast" every X seconds.
3cont- This process is mostly about taking powerful but not class defining goodies and ensuring all within a role have it. From here, we can take individual goodies and only compare them against other goodies within the role and adjust them as needed. Another specific example is that Machinist no longer has Tactician, as the -10%/90s mitigation for the party is a Marksman tool. Does the Machinist have enough goodies compared to the Black Mage and Samurai? If not, address it.
TLDR: Our current sorting system sucks, we need a better one for long term game health.