These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Name's the Same: Averted. In the X-COM series, the type-1 alien fighter is called the Wraith. To avoid confusion with the space vampires from Stargate Atlantis, the author decided to call them "Foo Fighters," after what pilots called UFO's during World War II.
There is a Jaffa Pilot named Ronan who appears briefly in chapter 41, who has a homophonous name to the Satedan Runner from Stargate Atlantis. However, given that the Jaffa never appears again, it's safe to say that the Jaffa Ronan will probably not have any meaningful impact on the story.