You'll probably be seeing unspoken alliances happen dynamically as the situation in the field changes. If say Chaos are making a push on the Eldar and Space Marines and they're winning and suddenly you turn it around and you have the Eldar and Space Marines attacking a vital chaos facility most people on those sides will probably choose to ignore each other. That is until chaos is evicted then they slaughter each other.
I think the only alliances will be along the lines of not invading territory owned by another Faction by mutual consent. Perhaps because the Eldar are on the SM border to the East and they are fighting off Chaos and the SM are being attacked on the West by Greenskins. You might see a non aggression pact between SM and the Pointy Ears. IB
Any alliance is heresy! And, moreover, will be broken. Nobody speaks on behalf of the entire faction, any alliances that are agreed will be negligible at best.
More referring to land take over as directed by the WC. I can certainly see some form of communication between some of the Factions where they agree not to land grab from each other for whatever reason. As for skirmishing... sure I don't care whether my power sword goes into Orc or Eldar IB
Yeah but you still can't control that. You will have Strike Forces and communities within factions that disagree with the War Council and will go grab land to spite them.