One problem with dropping Elidibus into the True Neutral or Neutral Dark categories is that, in addition to whatever "balancing" he's trying to do, he's unabashedly on board with the whole Rejoining plan. It bears repeating that the Rejoining requires the murder of countless billions of people. Perhaps it's humancentric thinking, but that solution is not a viable one, no matter how desperate the reason.
It could well be that Elidibus has knowledge that makes this the LOGICAL course of action. Perhaps the way the worlds are now, leaving them Unjoined will inevitably lead to the destruction of all of them. So, it's a "kill many to save a few, or kill no one and lose everyone" situation. From a purely logical perspective, it makes sense to save a few, rather than lose everyone.
Even if that's the case, though, the fact that he keeps his cards close to the chest indicate that he believes these logical reasons are ones he feels illogical beings would refuse to accept - that in their ignorance, they'll try to look for another solution, where there is none to be found. And he would be RIGHT - we WOULD look for another way. And maybe, in spite of all Elidibus's logic, we'd find one.
And maybe that solution would result in a situation where the Ascians are not on top, and Zodiark is not free. It is not to Elidibus's benefit to find an alternate solution, because the one they have is guaranteed to work, and will greatly benefit he and his kind in the bargain. All it requires is the extermination of a pestilence of lesser beings - humans - and honestly, wouldn't that be for the best, anyway?
No, all of the supposed duplicity Hydaelyn has exhibited so far is barely a candle's flicker in the face of Elidibus's blazing inferno. He may seek balance, but balance is not the end goal. The balance he seeks is one that supports other goals, and those other goals are not good for us, or any of the billions of beings like us.