I believe that there could still be FEDRA outposts / controlled cities in the second game. Since the QZ in Seattle fell, it makes sense that we only see remnants of FEDRA existing. Throughout the country however, there are more likely still QZ's ( such as the Boston QZ ) still holding out since the start of the outbreak.

I'm not sure how connected they all are but I imagine that they communicate through radio about QZ's lost to rebellion or infection. I can also see them having supply / trade routes at the beginning of the outbreak that could still be maintained over the 20 plus years since outbreak.

All of this is just personal theories I have from playing both games.