### 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)

}
					CapsuleShape3D *capsule = Object::cast_to<CapsuleShape3D>(*s);
					if (capsule) {
						Array arr;
						arr.resize(RS::ARRAY_MAX);
						CapsuleMesh::create_mesh_array(arr, capsule->get_radius(), capsule->get_height());
						_add_mesh_array(arr, transform, p_vertices, p_indices);
					}
					CylinderShape3D *cylinder = Object::cast_to<CylinderShape3D>(*s);
					if (cylinder) {
						Array arr;
						arr.resize(RS::ARRAY_MAX);
						CylinderMesh::create_mesh_array(arr, cylinder->get_radius(), cylinder->get_radius(), cylinder->get_height());
						_add_mesh_array(arr, transform, p_vertices, p_indices);
					}
					SphereShape3D *sphere = Object::cast_to<SphereShape3D>(*s);
					if (sphere) {
						Array arr;
						arr.resize(RS::ARRAY_MAX);
						SphereMesh::create_mesh_array(arr, sphere->get_radius(), sphere->get_radius() * 2.0);
						_add_mesh_array(arr, transform, p_vertices, p_indices);
					}
					ConcavePolygonShape3D *concave_polygon = Object::cast_to<ConcavePolygonShape3D>(*s);
					if (concave_polygon) {
						_add_faces(concave_polygon->get_faces(), transform, p_vertices, p_indices);
					}
					ConvexPolygonShape3D *convex_polygon = Object::cast_to<ConvexPolygonShape3D>(*s);
					if (convex_polygon) {
						Vector<Vector3> varr = Variant(convex_polygon->get_points());
						Geometry3D::MeshData md;