I assume the obstacles that you're talking about in Section 2 & 3 are smaller than the ones that have carved out portions of your navmesh in the example in Section 1. Is that right?
That, combined with the mention in Section 2 “The navigation mesh is built without taking buildings and other static objects into consideration”, my initial reaction/suggestion would be: Don't do that.
If your navmesh already reflects the nature of the static world geometry, why doesn't it also reflect the static nature of other static objects in the world? Is there some particular …