There's also the issue that the 'accident' at Galatia, that messed with Natural Jump points, was replicated by the Player, and is thus theoretically Weaponisable, and that most of the Factions occupy mainly systems with Gates in, meaning that any of them could be intentionally cut off from Hyperspace by a Hostile party.
This may well be why Scylla and Ella bailed - they're afraid not only of the Hegemony seizing and exploiting use of the Gates themselves for advantage, but also using this effect to Crush everyone else by locking them inside their own systems, with the only way in or out being use of the Gates or the relative handful of people who can Transverse Jump safely.
Of the Factions, we only know of the Hegemony, Via Galatia, that can currently use the Gates (in theory, if they can replicate the Janus device) and Tri-Tachyon that can reliably Transverse Jump, maybe, if they got it from the Defector before the extraction.
Other than that, Transverse Jump seems to be something that gets done by dangerous monkeying with the Drive rather than something that can be used reliably en masse, so in theory, the Hegemony, after seizing Galatia's work, could, if they replicate the first gate test effect, starve the rest of the sector into Compliance by bottling them up in their own systems by cutting off access to Hyperspace, and using the Gates against them...
And that's without even considering that if access to none of the Stars are Left...