Scarlett Johansson doesn’t look any different than we’re used to seeing her, so it’s possible the bulk of the movie could be set in the aftermath of Civil War, but with a few flashbacks to earlier points, perhaps showing us Natasha’s own origin story in a much deeper way than we got in Avengers: Age of Ultron.
The fact that the entire movie is a “flashback” from the point it takes place in our timeline, could simply mean that the movie might jump around in time more than we thought.