First off, we were told the amount of Rejoinings that have occurred and the status of the First and Thirteenth as being special by multiple sources including Hydaelyn and Elidibus, so I don't know why they would all lie about it.

The Lightning Calamity also doesn't match the timeline because that would've been many thousands of years ago, older than even the Allagan Empire. Even if you take into account time weirdness, that still doesn't add up in the timeline we were told and the amount of bending the timeline that would have to occur to have that all match up would be particularly egregious. The Milala left the Source to Alexandria's reflection thousands of years AFTER the Calamity of Lightning but arrived in Alexandria's shard BEFORE their lightning problem started.

The most likely case is that it's just another shard that hasn't been Rejoined. There are more elements than there are shards so they were bound to double-up on them eventually. Either way, looks like the lightning is somehow over in post-MSQ Living Memory, which is their shard and there's lightning somehow under the dome on the Source with no explanation how that works. But we'll probably find out in the patches.