To answer you points:
1) I will not deny that the Balance makes optimal openers, however with the people I talked to (I guess it's pretty much known that it was the mentors at this point), the concept of holding raid buffs seemed alien to nearly everyone. This leads me to believe that all the openers were made under the rule of using all buffs and bursts as early as possible and that the concept of holding raid buffs and allowing each class to get more of their bigger hits in the most buffs for a longer period of time wasn't really explored.
I'll repeat it again: I do very much encourage the use of early raid buff openers in fights where doing so will gain you an extra cast or prevent you from losing one. Case in point, for E3S, I believe the GNB opener starts its Gnashing combo on the 3rd GCD, much earlier than the usual openers, simply because doing so ensures that a Gnashing combo isn't lost due to Maelstrom. This fact alone makes it stronger overall in E3S (and in a vacuum). However, while it's possible for GNB to do this and follows the rule of "using burst phases as soon as possible", you usually wouldn't in other fights because the bulk of Gnashing misses a lot of raid buffs and using it 3 GCDs earlier probably won't gain you an extra usage of a Gnashing combo overall. This is the best example of my point where "if you can get the same number of casts off whether they're used early or not, then what's wrong with lining them up in a way that every class can make the most use of them?" I even gave a list on page 5 of this thread detailing the GCDs and oGCDs this alignment aims to fit in around 15secs.
2) Again, you say it's never optimal, but you don't really give a clear reason why. As for the example you give, the classes using the 2 minute raid buffs can only hold it for so long, otherwise they'll miss out on a duration of their buffs, which is what happens to all the other classes (now including NIN) regardless of how early their buffs are used in the opener. Even for DRG, which has the earliest raid buff usages in early raid openers, because you still lose out on a duration of their buffs by the end, you have to ask if that's really considered an extra cast. Also, while this might be fine for a speed run, in which you'd reset whenever someone dies, in a regular run where clearing is the goal, as soon as someone dies, that estimated kill time goes right out the window, making the possibility of retaining casts despite delaying raid buffs even higher.
Also, aside from DRG, most of the openers I list delay raid buffs and burst phases no more than 3 GCDs, so how likely are you to lose a cast in a full uptime fight like E2S?