### Godot version

4.1.beta3

### System information

Godot v4.1.beta3 - macOS 13.2.1 - Vulkan (Forward+) - dedicated AMD Radeon Pro 580 - Intel(R) Core(TM) i7-7700K CPU @ 4.20GHz (8 Threads)

### Issue description

When baking the mesh in GDScript after placing a Node3D (StaticBody3D with CollisionShape3D) these error message are displayed:

```
E 0:00:02:0733   update_polygons: Navigation map synchronization error. Attempted to update a navigation region with a navigation mesh that uses a different `cell_height` than the `cell_height` set on the navigation map.
  <C++ Source>   modules/navigation/nav_region.cpp:114 @ update_polygons()

E 0:00:19:0007   sync: Navigation map synchronization error. Attempted to merge a navigation mesh polygon edge with another already-merged edge. This is usually caused by crossing edges, overlapping polygons, or a mismatch of the NavigationMesh / NavigationPolygon baked 'cell_size' and navigation map 'cell_size'.
  <C++ Source>   modules/navigation/nav_map.cpp:770 @ sync()
```


**In Godot v4.1.beta2 it worked,** i.e. no error message

### Steps to reproduce

GDScript:
```
@onready var _navigationRegion3D: NavigationRegion3D = %NavigationRegion3D

:

_navigationRegion3D.bake_navigation_mesh(false)
```

Properties NavigationRegion3D:
<img width="434" alt="CleanShot 2023-06-22 at 19 15 44@2x" src="https://github.com/godotengine/godot/assets/1539838/30410b5f-99f1-40a4-82d4-2d6d66f673d5">


### Minimal reproduction project

[RTS 3D BakeIssue.zip](https://github.com/godotengine/godot/files/11839898/RTS.3D.BakeIssue.zip)

vertex_array.push_back(top_right);
										vertex_array.push_back(bottom_left);
										vertex_array.push_back(top_left);
										vertex_array.push_back(top_right);
										vertex_array.push_back(bottom_right);
										vertex_array.push_back(bottom_left);
									}
									map_data_current_index += 1;
								}
							}
							if (vertex_array.size() > 0) {
								_add_faces(vertex_array, shapes[i], p_vertices, p_indices);
							}
						}
					} break;
					default: {
						WARN_PRINT("Unsupported collision shape type.");
					} break;
				}
			}
		}
	}
#endif
	if (p_recurse_children) {
		for (int i = 0; i < p_node->get_child_count(); i++) {
			_parse_geometry(p_navmesh_transform, p_node->get_child(i), p_vertices, p_indices, p_generate_from, p_collision_mask, p_recurse_children);
		}
	}
}
NavigationMeshGenerator *NavigationMeshGenerator::get_singleton() {