It's dynamic. Finish an outpost in an area and it'll shift within that specific area. And once you clear a region, they're completely gone.
It's 90/10 because the Project at Eden's Gate just did a hostile takeover of the entire region. This is literally within a few days of the takeover. (If not the next day.)
Good point. Never even noticed that was happening after clearing out the outposts or areas. In fact, in John's region after I had progressed past 70% I felt like their attacks were getting worse but this time by airplane and helicopters. I had to jump over to Faith's region and clear another 2 levels of resistance to get the RAT4 which works like a charm.