### 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)

for (int i = 0; i < meshes.size(); i += 2) {
				Ref<Mesh> mesh = meshes[i + 1];
				if (mesh.is_valid()) {
					_add_mesh(mesh, p_navmesh_transform * xform * (Transform3D)meshes[i], p_vertices, p_indices);
				}
			}
		}
		if (p_generate_from != NavigationMesh::PARSED_GEOMETRY_MESH_INSTANCES && (gridmap->get_collision_layer() & p_collision_mask)) {
			Array shapes = gridmap->get_collision_shapes();
			for (int i = 0; i < shapes.size(); i += 2) {
				RID shape = shapes[i + 1];
				PhysicsServer3D::ShapeType type = PhysicsServer3D::get_singleton()->shape_get_type(shape);
				Variant data = PhysicsServer3D::get_singleton()->shape_get_data(shape);
				switch (type) {
					case PhysicsServer3D::SHAPE_SPHERE: {
						real_t radius = data;
						Array arr;
						arr.resize(RS::ARRAY_MAX);
						SphereMesh::create_mesh_array(arr, radius, radius * 2.0);
						_add_mesh_array(arr, shapes[i], p_vertices, p_indices);
					} break;
					case PhysicsServer3D::SHAPE_BOX: {
						Vector3 extents = data;
						Array arr;
						arr.resize(RS::ARRAY_MAX);
						BoxMesh::create_mesh_array(arr, extents * 2.0);
						_add_mesh_array(arr, shapes[i], p_vertices, p_indices);
					} break;
					case PhysicsServer3D::SHAPE_CAPSULE: {
						Dictionary dict = data;