Having completed the Galitan University story to unlock gate travel, I have a few theories about the gate network. My first one that I am very confident in is that the gate network is alive, my second, less confident one, is that the Domain was playing with alien tech.
As for 1, well the gates are described as having a heart beat once you get the Janus device. The first time you try and travel a gate in a non core system the failure is described as something screaming at you. I think that the gate network is alive somehow with my best guess that it woke up or got fed up when the gate network shut down. I don't think it likes being used.
For 2, well look at the designs for siphons, their guards, and the very redacted. Those bear some similarities to high-tech vessels, but they are undeniably alien about it. Its entirely possible that the gate network itself was alien in origin and the Domain stumbled upon them and claimed credit. Also, I believe that the siphons were likely a key in maintaining the gate network by providing the energy to keep it open. Those stations look alien and there is nothing else like them in the sector, save for the very redacted. I might hazard that these things were alien or built using alien tech, likely from the same people who built the gates. It would also explain the guards they have, those are things that I don't thing the Domain would have been happy to have on their siphons when a legion of ships built off the power of a star could have done fine. If the Domain did build the siphons, then they were somehow included in the schematics and no-one knew what the did.
Any way, that's my interpretation of the story.