I don't think of Mudokons and Birds having an agreement between them, I see them as being spiritually interwoven. Mudokons evolved from birds, and ever since the two species have shared an intimate relationship that goes beyond the physical world.
I'm probably talking a load of Koblenz, but that's how I see it.
I see Birds as being the soul of Mudokons. When Abe's body dies, we can see Birds flying out. That's his soul, ready to be resurrected. And I think bird portals are activated when Mudokons' Spooce awakens some dormant instinct in Birds to form a wormhole in space, much like Anna describes it another topic (the Gluk Evolution one I think).
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