Collected from pre-titans Galactic War system descriptions. I've attempted to put things into a rough timeline, but keep in mind it was originally presented in disjoint order, and my interpretation may be wrong. Too large for a single forum post, see file.
To clarify, so is it confirmed that progenitors are extinct? The last quote is pretty clear. Would have been nice to see a PA2 with a human faction derping around... Anyway I will continue to happily dream about th Imperium Of Man.
I didn't find any definitive statement about the outcome of the Pro-Com war. The ordering between NEST and Operation Kadota was also unclear. Kadota is especially interesting; it's apparently a type of fig, and also means "To disappear, vanish." So maybe the progenitors are hiding inside a planet somewhere. The lore sort of feels like it was setting the stage for three different army types if PA was successful enough.