LeftHandofGod I could answer this in two ways:
First, I notified everyone who approached the borders that ftl within the borders is most likely hazarous of not deadly, due to the sub-space particles that followed the apocalypse, the will latch onto ships, move into engines, they´re thin spread but have enough density and energy to grind everything to dust that tries to enter ftl within the terriotry, if it is not immediatly detonated or evaporated by the friction and energy potential once they are triggered, should someone try to open agat eor Portal of whatever sorts, the particles would also enter this and make it collapse upon itself due to the heavy strains the high energy potential put on the gate or tunnel of sorts, it might also happen that the area around the side might be infested with the same particles in the process.
Second, I did predict that the Imperium would use the FTl jump, as there had been no obvious ways to escape and from what I´ve seen the Imperium prefers an by their standards honorful death over a defeat of whatever kin dit may be, aswell their emergency protocols state to erase all data and (if I remmeber right) use the self-destruction in a case of being captured, though as they knew of the subspace particles there was a much more efficent way to handle the self-destruction: entering ftl and destroying everything in the near vicinity, it was a logical course of action for the Imperium.