I'll be taking a page from Warhammer Fantasy, where the Immaterium is really a well of magic that pours into reality. When tears to the warp were created by certain apocalyptic events in history, this magic flowed freely into the universe. The magically inclined who could control this new power became magnified in their abilities; while those who couldn't became uncontrolled conduits of magic, becoming a danger to everything.



In Equestria, a great distrust of unicorns began to grow after the part they played in the Age of Strife. While Celestia tried her best to protect the unicorns from that stigma, her disappearance after the events of the Luna Heresy led organisations, such as the Ordo Hereticus, to hunt down and persecute unsanctioned unicorns, leading to a great depletion of their numbers in Equestrian society.



I haven't quite nailed down what I'd do about astropathic messages, but I'm pretty sure there will be unicorns who will fulfil that task as Astropaths.



The upkeep of the Astronomicon is also something I haven't quite nailed down yet, but I won't be surprised if Equestria would condone such sacrifices. The Ponyhammer universe is pretty bleak, and sacrifices will have to be made, even if it goes against everything they believe in.