### 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)

if (Object::cast_to<MeshInstance3D>(p_node) && p_generate_from != NavigationMesh::PARSED_GEOMETRY_STATIC_COLLIDERS) {
		MeshInstance3D *mesh_instance = Object::cast_to<MeshInstance3D>(p_node);
		Ref<Mesh> mesh = mesh_instance->get_mesh();
		if (mesh.is_valid()) {
			_add_mesh(mesh, p_navmesh_transform * mesh_instance->get_global_transform(), p_vertices, p_indices);
		}
	}
	if (Object::cast_to<MultiMeshInstance3D>(p_node) && p_generate_from != NavigationMesh::PARSED_GEOMETRY_STATIC_COLLIDERS) {
		MultiMeshInstance3D *multimesh_instance = Object::cast_to<MultiMeshInstance3D>(p_node);
		Ref<MultiMesh> multimesh = multimesh_instance->get_multimesh();
		if (multimesh.is_valid()) {
			Ref<Mesh> mesh = multimesh->get_mesh();
			if (mesh.is_valid()) {
				int n = multimesh->get_visible_instance_count();
				if (n == -1) {
					n = multimesh->get_instance_count();
				}
				for (int i = 0; i < n; i++) {
					_add_mesh(mesh, p_navmesh_transform * multimesh_instance->get_global_transform() * multimesh->get_instance_transform(i), p_vertices, p_indices);
				}
			}
		}
	}
#ifdef MODULE_CSG_ENABLED
	if (Object::cast_to<CSGShape3D>(p_node) && p_generate_from != NavigationMesh::PARSED_GEOMETRY_STATIC_COLLIDERS) {
		CSGShape3D *csg_shape = Object::cast_to<CSGShape3D>(p_node);
		Array meshes = csg_shape->get_meshes();