NavigationAgent edge-centered path postprocessing forces each path point in the middle of any crossed-edge along the path. It has limited use outside of projects that use fixed layouts like square tile or hex games due to all the path detours it creates when the edges are not same sized everywhere.
Physics colliders are never directly taken into account by the navigation system as they are part of a different engine system, the physics engine. What the 2D navigation mesh baking does is that it parses the physics shapes to convert it into data that the navigation system actually uses, in this case the navigation mesh surfaces. That is why every change of a physics shape requires a new bake, by default a physics engine change does nothing for the navigation system.