### 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)

}
					} break;
					case PhysicsServer3D::SHAPE_CONCAVE_POLYGON: {
						Dictionary dict = data;
						PackedVector3Array faces = Variant(dict["faces"]);
						_add_faces(faces, shapes[i], p_vertices, p_indices);
					} break;
					case PhysicsServer3D::SHAPE_HEIGHTMAP: {
						Dictionary dict = data;
						
						int heightmap_depth = dict["depth"];
						int heightmap_width = dict["width"];
						if (heightmap_depth >= 2 && heightmap_width >= 2) {
							const Vector<real_t> &map_data = dict["heights"];
							Vector2 heightmap_gridsize(heightmap_width - 1, heightmap_depth - 1);
							Vector2 start = heightmap_gridsize * -0.5;
							Vector<Vector3> vertex_array;
							vertex_array.resize((heightmap_depth - 1) * (heightmap_width - 1) * 6);
							int map_data_current_index = 0;
							for (int d = 0; d < heightmap_depth; d++) {
								for (int w = 0; w < heightmap_width; w++) {
									if (map_data_current_index + 1 + heightmap_depth < map_data.size()) {
										float top_left_height = map_data[map_data_current_index];
										float top_right_height = map_data[map_data_current_index + 1];
										float bottom_left_height = map_data[map_data_current_index + heightmap_depth];
										float bottom_right_height = map_data[map_data_current_index + 1 + heightmap_depth];
										Vector3 top_left = Vector3(start.x + w, top_left_height, start.y + d);
										Vector3 top_right = Vector3(start.x + w + 1.0, top_right_height, start.y + d);
										Vector3 bottom_left = Vector3(start.x + w, bottom_left_height, start.y + d + 1.0);
										Vector3 bottom_right = Vector3(start.x + w + 1.0, bottom_right_height, start.y + d + 1.0);