Which is true, to a degree. Paladin was a weird job in that it was buffed for the vast majority of it's GCDs, so you could make the argument that it was no wonder it all lined up, because the chances of it not are slim. In a different mindset, this buffed damage was PLD's baseline, with a boost during Req and a slight dip when there is no FoF or Req.
However, temp raid buffs could potentially hinder job diversity. Imagine for a second 2 burst DPS, one where the buffed period is fixed, like Dragoon and another where it could be more flexible, as an example, take Monk, remove RoF and Brotherhood and make Perfect Balance and Masterful Blitz the burst window for Monk (with Perfect balance boosting damage). With perfect balance, you can be very very flexible with were you burst in a vacuum, you could delay it for an important ADD to take down as an example. Dragoon is as it is now (minus Battle Litany for this example).
If I now introduce a job that has a raid buff, the Monk is now going to want to put it's burst damage in that window, necessarily restricting where it can burst and losing that previous flexibility. Whilst Dragoon is hoping that the timing's on their burst window line up with the raid buff to make full use of it.
This is why I bought up Ninja in my post as it was the first job to have a universal raid (de)buff (Foe's Requiem was magic only) and that one debuff alone necessarily wanted people to make full use of it. We didn't have the insane potencies we have now, but it was still a factor. It causes jobs to funnel into that window, which is the same path that got us to where we are now.
As for ShB, being the last expansion before the 2 minute meta, most jobs were already 60/120 second jobs, with 90 second being uncommon and 180 being even rarer. But this is where the problem arises. Why should I bring the 90 second job when I can replace it with the 60 second job and get more damage out of it? That raid buff at 90 second is only really benefitting that one job and the odd action here and there. It is just in this weird, awkward spot. Maybe, shove it into the 120 second window? Just so it feels a but better to use. So again, we are shoving things into the raid window.
We could make some jobs 60/120, some 90 in about a roughly equal split, but could that then split the jobs down the middle, only wanting to party with jobs of their own buff timings? Would adjusting a job to fit both make it over/under powered in either one?
So it comes down to 2 main reasons why I do think they should go. The first being, we tried it, and throughout the expansions, it just kept getting shoved into the 2 minute meta it is now. It could end in a 3 minute meta if done differently, but it would still be the same complaints. The second, it necessarily reduces how you can build a jobs damage profile. By making these raid buffs, you are saying, dump all high potency attacks here, even if you job really doesn't want to. You kill the ability to provide flexibility in some jobs and diversify the way jobs do their damage.
Note, that this doesn't stop raid buffs going out, just ones that provide an increase in damage. Arcane Circle and Brotherhood are raid buffs that rely on the rest of the team to buff the job using them. There is also the case of keeping raid buffs up 100% of the time can be something that the job has to maintain by pressing more than just 1 button.
This all being said, there is no real right or wrong answer to this dilemma. Different people are going to have different opinions about what they think is the right direction, which does highlight the fact this is a more complex matter than it might initially seem.