As they would--the fact that the Altair ruins in the FS1 Monologues state that they're leaving the system (they said they would fall back and try to defend--perhaps the Knossos was an attempt to defend) suggest to me that T/V space was Ancients space--as the Ancients retreated, the Shivans followed. Shivans attack, Ancients defend, Ancients retreat. Rinse and repeat.
We know that the Ancients used to have a presence beyond Capella, Gamma Draconis, the Nebula, and the Binary System--that suggests to me that the T/V space was a central hub of Ancient space. It is likely much of Ancients space was evacuated, they left in various directions. I think it's suggested that their homeworld was beyond Ross 128. They built a Knossos, defended as well as they could, and activated the Knossos once defeat was unstoppable. That would lock the Shivans from leaving the system and preventing more from entering later. I think the node-map suggests that the average system has 3 to 4 jump nodes... on that, why would some more-outer systems be lacking in a node? Look at and beyond Ross 128, Mirfak, Regulus, and Aldebaran... they are seemingly lacking jump nodes.
I think it's possible that the Ancients ended up mass-producing the various parts of Knossos portals--the 4 "large" portions and the four "small" portions are all seemingly the same--they could produce those parts quickly and more easily then warships that will be destroyed quickly. They would refine the design after every Knossos device ended up failing. The Shivans continue the assult, the Ancients continue setting up and properly calibrating the Knossos devices.
One last thing, Stormkeeper, they kept retreating from hundreds of systems. The GTVA had about 30 systems... the Ancients had to have had at least 100--I'd think more-accurately that they'd have 500! T/V space had to have at least a few Ancients outposts. Upon the invasion and destruction of the Binary system (leading to their core systems), they likely setup more Knossos, in advance. Once they construct the devices, they would likely calibrate them to work properly. In their haste, they failed to calibrate all the Knossos devices to seal the nodes. Once the Shivans would break though (the monologue suggests to me that the Ancients had the ability to block nodes from the Shivans for a length of time, perhaps a year or more, as they fell back) the node, they moved back. The three nodes we see in most of the game is a last-ditch effort to stall the Shivans long enough to evacuate the core systems. Upon evacuation, chaos likely broke out. Many Ancients tried to return to the core systems and make a run to the homeworld. Others disagreed on where to go--they split up and went to many systems. They end up constructing several more Knossos to close the path to them.