My theory regarding the nebula is that the supernova that created it was a natural event. The Ancients built the Knossos as a way to travel there to harvest the nebular gasses to power their ships. This was where they encountered the Shivans.
Regarding the weapon test, what if the Shivans kill the Ancients, then go after the Terrans and Vasudans in FS1, get beat, decide to try to whack another race, in the process testing their supernova weapon, it fails, as a result they have bitten off more than they can chew and start to get owned, end up fleeing through Terran space to Capella, test the weapon again, get it working, and finally jump out to take another shot at the unknown race. (Excuse the run on sentence Goob.)
It would mean that they were building Sathani since the time they killed the Ancients, and just finished a few months before fleeing through Terran space. I believe FS2 also states the Shivans were less interested in controlling nodes this time through, reinforcing the idea that they were running from something.