Your idea that the Ivalice-timeline would include FF14 at all is probably the problem here.
Even though we're getting all this Ivalice-stuff, FF14 is not part of Ivalice - which in turn allows them a certain freedom. They dont have to stick to every detail and letter of the Ivalice-setting and can instead borrow the things they like or can use.
If it works better for them to have Rabanstre above Limberry/Lesia, then thats how that is in FF14.

Those raids are referencing the old games, they're not supposed to mimic them 1:1. They're drawing inspiration from the whole of Ivalice - sometimes, FFT might work better for a location, a boss or an NPC, sometimes its gonna be FF12, while twisting it in a way that it works within the FF14-lore.
Just how they've changed stuff about Crystal Tower and Xande compared to FF3 to make it work in FF14.

This works, because the Ivalice-rules dont apply to FF14 because FF14 isnt part of Ivalice.

We might learn more about Rabanstre and Lesalia in the context of the FF14-lore, but that wont be related to the FFT/FF12-timeline.