### 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)

#ifndef _3D_DISABLED
#include "navigation_mesh_generator.h"
#include "core/math/convex_hull.h"
#include "core/os/thread.h"
#include "scene/3d/mesh_instance_3d.h"
#include "scene/3d/multimesh_instance_3d.h"
#include "scene/3d/physics_body_3d.h"
#include "scene/resources/box_shape_3d.h"
#include "scene/resources/capsule_shape_3d.h"
#include "scene/resources/concave_polygon_shape_3d.h"
#include "scene/resources/convex_polygon_shape_3d.h"
#include "scene/resources/cylinder_shape_3d.h"
#include "scene/resources/height_map_shape_3d.h"
#include "scene/resources/navigation_mesh_source_geometry_data_3d.h"
#include "scene/resources/primitive_meshes.h"
#include "scene/resources/shape_3d.h"
#include "scene/resources/sphere_shape_3d.h"
#include "scene/resources/world_boundary_shape_3d.h"
#ifdef TOOLS_ENABLED
#include "editor/editor_node.h"
#endif
#include "modules/modules_enabled.gen.h"