I feel like some kind of ancient guru at the top of a mountain dispensing wisdom from on high...

I am admittedly a titch rusty on my Freespace history, but I will see what I can do...
From what I remember from the original game(s), the Knossos gates were not made by the Shivans, but from an ancient race that predate even the Shivans. Presumably, the Shivans don't have the technological knowhow to build a Knossos gate. Granted, I took some liberty with that with Derelict, and presented the idea that they could re-open a collapsed node, only if they had "access" to both sides of it. In the original storyline, when Capella collapsed, there were no large Shivan ships in GTVA space outside of the Capellan system, so they wouldn't be able to re-open it.
The idea with Derelict, is that the principle threat of the Nyarlathotep was that it was capable of re-opening collapsed nodes... and reopen the floodgates of a new unstoppable Shivan invasion... The Shivan-skinned Knossos gate in Derelict was a way to symbolize that...
Does that work for an explanation? I'd almost have to go back and replay my own campaign to refresh my memory

Oh... and
what Owl incident?