that honestly sounds really dumb, and I hate this...
The way the game's mechanics work, it's not dumb, but actually in line with existing mechanics. Yma is claimed by the pirates. If you settle there, they'll be the ones attacking your colony. But if you decivilize Qaras, the pirate claim goes away, and it becomes claimed by the Persean League, because now Salamanca is the largest remaining settlement. So logically, while the Hegemony and Church might initially be claiming the uninhabited core world systems, once your colony is built there, you should be the one with the claim. And while it does make sense that they might go after the colony initially, once it's reached Size 5 and is no longer a valid target for saturation expeditions, it would make sense that you're now the one with the claim on the system.
Though whatever, I could be wrong. Why do you want to colonise a Core World system anyway???
... because they're the most profitable due to highest accessibility? If you get a Penelope's Star roll with farmland on Ithaca and organics on Xuthus that is basically the best possible system you can get, barring one of those (very rare) cases where a non-core system with good planets spawns right next to the core.