Yeah, WYLB was put together poorly. The Dukat/Winn parts long like they are over minutes/hours while you have the crew section over days at least, which makes the timeline confusing if you actually think about it.
I've kind of "fanwanked" the explanation into assuming that there is a time dilation effect going on in the Fire Caves, that because of the Pah-Wraiths' active presence, there were effects similar to what you would get at relativistic speeds.
But I don't think that explanation should've been necessary.
Sorry, I should have clarified. Until "What you leave behind" I don't think Dukat ever truly encountered a Pah-Wraith, so up till that point his motives to release them should've been entirely selfish and for himself with no real devotion to them. Then when Winn kills him and they revive him, he's nothing more than their possessed puppet.
That's not correct, actually. In "Tears of the Prophets," he did
actually absorb one into his body and become possessed by it. You may observe that when he shows up on DS9, he doesn't show normal humanoid behavior (well, as normal as Dukat gets) until after the Pah-Wraith flows out of him and into the Orb. It's only after that, that he speaks or shows some sort of emotion other than the Pah-Wraiths' pure malevolence.
The events of "Covenant" occur after
the first incident where he was possessed; that's why I think the Pah-Wraith that possessed him the first time left him permanently lacking free will where the Pah-Wraiths are concerned.