It's actually quite simple. A base is assumed to be hostile until proven otherwise. Magellan, as stated before, is a border system between Bretonia and Liberty, and is patrolled by both houses (mainly the navy keeping an eye on things). IMG also has a stake in the system, at Freeport 4.
If you build a base there without notifying the houses, and a patrol happens upon it, then it would be considered a potential threat to the security of both houses. As a result, the response by those houses is a short ultimatum and fine (to prevent the base owner from building up to prepare for a siege), and in some cases, an immediate destruction. Frankly, I find that perfectly normal. Unknown/unregistered base? Pirate hive -> Destroy it. That you failed to do some research before plopping down a huge investment is, frankly, player error, not a rule violation of any kind.
And no, there are to my knowledge, no systems in Discovery that do not fall within the sphere of influence of any faction. The deep Omegas and Taus come close, but you still have the Hessians/Corsairs (omegas) and Outcasts/Gauls (Taus) to deal with.
Wide awake in a world that sleeps, enduring thoughts, enduring scenes. The knowledge of what is yet to come.
From a time when all seems lost, from a dead man to a world, without restraint, unafraid and free.
Mostly retired Discovery member. May still visit from time to time.