### 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 (p_navigation_mesh.is_valid()) {
		p_navigation_mesh->clear_polygons();
		p_navigation_mesh->set_vertices(Vector<Vector3>());
	}
}
void NavigationMeshGenerator::parse_source_geometry_data(const Ref<NavigationMesh> &p_navigation_mesh, Ref<NavigationMeshSourceGeometryData3D> p_source_geometry_data, Node *p_root_node, const Callable &p_callback) {
	ERR_FAIL_COND_MSG(!Thread::is_main_thread(), "The SceneTree can only be parsed on the main thread. Call this function from the main thread or use call_deferred().");
	ERR_FAIL_COND_MSG(!p_navigation_mesh.is_valid(), "Invalid navigation mesh.");
	ERR_FAIL_COND_MSG(p_root_node == nullptr, "No parsing root node specified.");
	ERR_FAIL_COND_MSG(!p_root_node->is_inside_tree(), "The root node needs to be inside the SceneTree.");
	Vector<float> vertices;
	Vector<int> indices;
	List<Node *> parse_nodes;
	if (p_navigation_mesh->get_source_geometry_mode() == NavigationMesh::SOURCE_GEOMETRY_ROOT_NODE_CHILDREN) {
		parse_nodes.push_back(p_root_node);
	} else {
		p_root_node->get_tree()->get_nodes_in_group(p_navigation_mesh->get_source_group_name(), &parse_nodes);
	}
	Transform3D navmesh_xform = Transform3D();
	if (Object::cast_to<Node3D>(p_root_node)) {
		navmesh_xform = Object::cast_to<Node3D>(p_root_node)->get_global_transform().affine_inverse();
	}
	for (Node *E : parse_nodes) {
		NavigationMesh::ParsedGeometryType geometry_type = p_navigation_mesh->get_parsed_geometry_type();
		uint32_t collision_mask = p_navigation_mesh->get_collision_mask();
		bool recurse_children = p_navigation_mesh->get_source_geometry_mode() != NavigationMesh::SOURCE_GEOMETRY_GROUPS_EXPLICIT;
		_parse_geometry(navmesh_xform, E, vertices, indices, geometry_type, collision_mask, recurse_children);
	}
	p_source_geometry_data->set_vertices(vertices);
	p_source_geometry_data->set_indices(indices);