Ascian methodology is literally creating an aetheric imbalance so that it would break the world between dimensions so they're pulled back in the Source. We know they have been messing with shards to prime them for Rejoining at least as early as when the Void was created, so at the very minimum before Allag (I don't think we have mentions of Voidsent before that?), so a Shard being close to a calamity state isn't a stretch at all. They're most likely all already somewhat unbalanced and near the tipping point to be merged if the occasion presents itself on the Source. Black Rose succeeded in fucking up the Source in an alternate timeline.
The lightning devastation on the continent was triggerd by Lindblum's superweapon. It was described as engulfing the continent, not the whole world. Not sure how Alexandria would know that, though.
Either it was an Ascian plan, or Lindblum went overboard with it and just caused widespread mass destruction. It's not unheard of: Koryu almost caused a mass destruction event on the Source, unrelated to any Ascian plot as far as we know.
I'm not sure where you gathered that the rest of the world was vaporized, but Sphene says in one of the first quest in Heritage Found that they had no idea what happened outside of the dome before Zoraal Ja went through. If you have a specific NPC dialog or quest mentioning it, I'm very interested, that might put things in a new light.
However, I disagree that the game makes you assume the shard got rejoined:They actually make sure you understand it's not one of them. The only link is Lightning, and since there's only 6 elements plus Light / Darkness, they will obviously overlap at some point.
- Y'shotla directly mentions it leads to one of the Reflection ;
- We're told since the beginning that rejoined Reflections are totally gone ;
- At no point do they speculate it could be a rejoined shard, and all Scions know that one shard fell to lightning ;
- The interdimensional fusion is described as being able to merge a reflection with another, not drifting part of land in the interdimensional rift ;