I think a big key here is the briefing text from Mystery of the Trinity:
We have travelled (sic) farther than any Terrans in the history of subspace travel.
Of course, we know the Trinity made it first, but it still stands; Lt. Samsa had a reason for saying that. Was it they knew the exact location of the nebula from the stars (somehow) or other navigational equipment, like subspace tracking? Did it take a much longer time than a normal jump? I say the latter, but it doesn't really matter. I don't think it was a case of Sam Gamgee saying "If I take one more step, I'll be further away from home than I've ever been." They were much further away from home then they've every been. I believe that the Knossos can create a subspace tunnel that couldn't form naturally. Now, is it to the other side of the galaxy, no.
So it is obvious that the Ancients specifically chose that system to set their Knossos to (and build another one in it). Now, if it was already a nebula when they found it, the only reason I can see is they found it to be a good hiding spot from the Shivans or their lesser enemies. Sure, they could have used it for gas mining, but the Knossos "chain" that goes through there suggests a trade route or military highway.
If the system wasn't a nebula initially, it could have been a colony or manufacturing facility. When the Shivans (presumably) made the star go nova, the Knossos could have survived. It could have been built like a Mass Relay, but then someone would have to "catch" it. More likely is it was destroyed and the Ancients simply rebuilt it.