It could be a bit of both. However, in one of the LLs leading up to Endwalker, I recall Yoshida directly saying they wanted to make buff alignment easier and that was the reason for shifting everything to two minutes.
If I were to hazard a guess, they only realized after how difficult it was to actually balance everything with so many abilities being forced into this two minute meta and/or there were concerns with players forgetting to align 90s abilities. So they gradually started shaving more of them down as it became far too late in development to scrap the whole system. This is why we saw a few hold overs like Bloodfest and Leylines. Both those abilities add credence to the theory as they simply didn't work anymore, making it much harder to properly optimize. It wouldn't be the first time they made changes without rhythm or reason. Case in point, Bard. After years of begging and pleading for Bloodletter charges, Bard mains finally got them... only to remove the entire reason they wanted them in the first place. This disconnect meant people complained and the dev team threw up their hands, wrongly assuming the players don't know what they want.
Considering the woefully poor balance we've seen throughout Endwalker, it really does make one wonder how much testing they did or how exactly they test jobs.
Chief among them being Direct Hit and the now abundance of ridiculously high potency skills which lead to absurd swings in damage. Having two layers of RNG is, frankly, dumb. Nevertheless, it's the high potency skills that are the real issue. A Ninja shouldn't see Hyosho flux between 80k and 170k because they just happened to roll lucky that pull. While that could happen in Shadowbringers, most jobs lacked the big hits and it wasn't nearly as impactful because buffs were more spaced out. A weak Hyosho at the two minute window could level itself out if you crit during the one or three minutes as you were likely running into buffs such as Litany or Battle Voice. Now you're wholly dependent on two minutes exactly. I've seen myself dip upwards of nearly 1,000 rDPS on Paladin simply because my blade combo and/or Goring Blade just didn't not to crit at all. Same exact rotation. Game said go fly a kite.
So while the two minute meta remains awful, I'd also like to see them abandon Direct Hit and stop with the fat potency skills. Sadly, I suspect come 7.0 they're just going to make them all auto DHC, which I guess solves the problem but kind of defeats the point of even having modifiers.