Thoughts on how we might go from WoL to WoD

[Cilia]

iirc during the WoDs plot in Heavensward their goal was to kill each beast tribe's primal as many times as they can until the ascians can goad them to pray to Zodiark instead so I assumed it was Zodiark that gave them the power of darkness

Not per sé. The goal was to have the Warriors of Darkness kill primals to the point the beastmen had to collectively create a new god (primal) to protect them - one more powerful than their individual gods. Though the Warriors of Darkness ultimately failed in this endeavor, Ilberd succeeded with the added bonus of starting a war with the Empire.

Zodiark Himself never factored into it.

.........then again you can become a dark knight while being at Hydaelyn's side so it's a bit confusing

The difference is that Dark Knights wield their own darkness - or more accurately their hearts, negativity and all - as a weapon, as opposed to wielding Zodiark's divine power of Darkness.