### 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)

return singleton;
}
NavigationMeshGenerator::NavigationMeshGenerator() {
	singleton = this;
}
NavigationMeshGenerator::~NavigationMeshGenerator() {
}
void NavigationMeshGenerator::bake(const Ref<NavigationMesh> &p_navigation_mesh, Node *p_root_node) {
	WARN_PRINT_ONCE("NavigationMeshGenerator::bake() is deprecated due to core threading changes. To upgrade existing code, first create a NavigationMeshSourceGeometryData3D resource. Use this resource with method parse_source_geometry_data() to parse the SceneTree for nodes that should contribute to the navigation mesh baking. The SceneTree parsing needs to happen on the main thread. After the parsing is finished use the resource with method bake_from_source_geometry_data() to bake a navigation mesh..");
}
void NavigationMeshGenerator::clear(Ref<NavigationMesh> p_navigation_mesh) {