### 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 (!meshes.is_empty()) {
			Ref<Mesh> mesh = meshes[1];
			if (mesh.is_valid()) {
				_add_mesh(mesh, p_navmesh_transform * csg_shape->get_global_transform(), p_vertices, p_indices);
			}
		}
	}
#endif
	if (Object::cast_to<StaticBody3D>(p_node) && p_generate_from != NavigationMesh::PARSED_GEOMETRY_MESH_INSTANCES) {
		StaticBody3D *static_body = Object::cast_to<StaticBody3D>(p_node);
		if (static_body->get_collision_layer() & p_collision_mask) {
			List<uint32_t> shape_owners;
			static_body->get_shape_owners(&shape_owners);
			for (uint32_t shape_owner : shape_owners) {
				if (static_body->is_shape_owner_disabled(shape_owner)) {
					continue;
				}
				const int shape_count = static_body->shape_owner_get_shape_count(shape_owner);
				for (int i = 0; i < shape_count; i++) {
					Ref<Shape3D> s = static_body->shape_owner_get_shape(shape_owner, i);
					if (s.is_null()) {
						continue;
					}
					const Transform3D transform = p_navmesh_transform * static_body->get_global_transform() * static_body->shape_owner_get_transform(shape_owner);
					BoxShape3D *box = Object::cast_to<BoxShape3D>(*s);
					if (box) {
						Array arr;
						arr.resize(RS::ARRAY_MAX);
						BoxMesh::create_mesh_array(arr, box->get_size());
						_add_mesh_array(arr, transform, p_vertices, p_indices);