While I would agree that no two jobs should play the same, I am also of the opinion that no job should be left out of certain content just because it happens to lack some sort of utility. I will try and expand further by providing an example, in this case tank stuns/silence/interrupt.

Back in ARR and HW, all tanks could stun, they all done it differently, but they all could, however, only 1 could silence, that being PLD. This could in theory exclude certain groups from certain things, as an example having a DRK/WAR tank combo but needing a silence. When they made role skills, they added the capability to both stun and silence to all tanks. This would (in theory at least) mean any content that requires a silence or a stun, no matter what tank combination you pick, you would have access to the required utility. The fact the game really doesn't utilise this fact in raids is disappointing, but it doesn't stop the case that theoretically, they could design content with that in mind.

Going to Job specialisations, an example was tank. You can either go more defensive or more damage, with the idea that certain content would require one or the other. However I would counter and say, what about when you get more gear? Suddenly, that fight that required a more defensive kit can be more offensive. Every fight (excluding Ultimates) will get easier as you upgrade your gear through the raids. This results in less defensive play and more offensive, which means, by the end of the tier, that fight you designed to be defensive orientated is now being fought with an offensive build. But you have to also remember you have to tune the fights for the lowest ilevel set for the raid, so just putting up big numbers doesn't help.

There was mention of putting multiple esuna curing status on the main tank, then do a raid wide. Assuming the debuffs will make the tank be hit very hard by the raid wide, there is a simple solution. Tank swap, mitigate the damage and pre-plan. Since fights are scripted, you can prep with an AoE shield, then, the tank gets the debuffs, healers can esuna while the tanks mitigate the damage and depending on the debuff, the tanks can swap, AoE goes out, healers heal up. Again remembering the AoE cannot be strong enough to kill the party but at the same time, you need to have enough time to remove the worst debuffs before the AoE comes out.

Everything is a fine balancing act around tanks, healers and DPS. I would also argue that designing fights around a specific skill set reduces the customisation as you are still required to have X, Y and Z, meaning there is really no choice. I might not have articulated my points in the most comprehensible manor, things sound good in my head, but they might not translate well over text, but I hope you can see the view point I am trying to get across.

TL;DR, some amount of homogenisation is good and skill trees are again an illusion of choice, even if you design content around specific sets.