I haven't personally tested the mod with Extinction Core so I can only speculate on how they'll behave together. I'm fairly certain that as a core mod, Extinction Core must always be first in the load order. Unfortunately, this mod is currently not able to force wyverns to spawn in nests by itself, it sort of piggybacks off other mods that do have this capability and just modifies the eggs that are laid. I am working on that flaw, but it's a much harder problem to solve than one would think xD. So since Extinction Core does not spawn nests, Agile Wyverns will not be able to spawn nests unless there is another mod on the server that enables it.

As for whether the Agile Wyverns will spawn with Extinction Core, I can't say for sure. I don't believe they will automatically replace the normal ones like they do without a core mod, but depending on how EC handles their dinos, they might. What I would guess will happen is either 1. Agile Wyverns will not be spawned naturally in the game at all but can still be force-summoned by an admin, 2. Agile Wyverns will spawn alongside the normal ones, or (least likely) 3. Agile Wyverns will attempt to replace normal wyverns and things may or may not break.

I would be interested to know the results if you end up experimenting with this.