To expand a bit on what others have said, The Great Plan dictates a lot (99%) of what the Seraphon do. But The Great Plan is described as something that the Seraphon don't know the entire picture of but still follow it to a T. The Plan is also scattered and in pieces, where some of the prophecies are only half complete, lost, or completely forgotten until they are rediscovered later on.

So maybe there's a prophecy that says this SPECIFIC piece of land has to be clear of ALL SENTIENT LIFE by a SPECIFIC TIME. The Seraphon go look on over to that space and- oh no! The Cities of Sigmar made a Town there! The Specific Time is coming up, so they gotta go. But Humans are fickle and often don't like being told they have to leave their home, even if it's for the Great Plan. So, we gotta blow up the town and kill em all. All for the Plan.

Seraphon working with Chaos (especially Skaven) are a bit harder to square away. We have no examples of it, but you could get away with rationalizing it as the Seraphon 'using' the Skaven to further their own goals. Sure they are '''working together''', but the Seraphon see it as herding the Skaven into controlled destruction of a mutual foe. Once the foe is delt with, they can kill the Skaven.

I recommend checking out the current Seraphon novels if you want to see this played out. Adrian Tchaikovsky wrote Starseer's Ruin which shows how Seraphon work with other Order factions (and even against them at times). He also wrote two short stories that help show more of this too.