The YoRHa raids are a pseudo-sequel to Nier: Automata. One of the endings of that game has the minds of its characters being uploaded into the sphere that then launches off into the cosmos in search of new worlds. One of the fears expressed by other characters is that the central conflict of Automata will simply be repeated on whatever world the sphere arrives at. Well, the sphere landed on the First and that's exactly what happened. In a way, not understanding what is going on is appropriate because the WoL and the dwarves are only seeing a tiny fraction of a larger story that's been going on long before they came to Norvrandt and will continue long after the raid is finished.

But you're right, the raid series is mostly it's own self-contained story that doesn't really matter to the wider setting or narrative. If you wanted to ignore something in FF14's lore, Dark Apocalypse is a good choice.