### 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)

ERR_CONTINUE(mesh_vertices.is_empty());
		const Vector3 *vr = mesh_vertices.ptr();
		if (p_mesh->surface_get_format(i) & Mesh::ARRAY_FORMAT_INDEX) {
			Vector<int> mesh_indices = a[Mesh::ARRAY_INDEX];
			ERR_CONTINUE(mesh_indices.is_empty() || (mesh_indices.size() != index_count));
			const int *ir = mesh_indices.ptr();
			for (int j = 0; j < mesh_vertices.size(); j++) {
				_add_vertex(p_xform.xform(vr[j]), p_vertices);
			}
			for (int j = 0; j < face_count; j++) {
				
				p_indices.push_back(current_vertex_count + (ir[j * 3 + 0]));
				p_indices.push_back(current_vertex_count + (ir[j * 3 + 2]));
				p_indices.push_back(current_vertex_count + (ir[j * 3 + 1]));
			}
		} else {
			ERR_CONTINUE(mesh_vertices.size() != index_count);
			face_count = mesh_vertices.size() / 3;
			for (int j = 0; j < face_count; j++) {
				_add_vertex(p_xform.xform(vr[j * 3 + 0]), p_vertices);
				_add_vertex(p_xform.xform(vr[j * 3 + 2]), p_vertices);
				_add_vertex(p_xform.xform(vr[j * 3 + 1]), p_vertices);
				p_indices.push_back(current_vertex_count + (j * 3 + 0));
				p_indices.push_back(current_vertex_count + (j * 3 + 1));
				p_indices.push_back(current_vertex_count + (j * 3 + 2));
			}
		}
	}
}
void NavigationMeshGenerator::_add_mesh_array(const Array &p_array, const Transform3D &p_xform, Vector<float> &p_vertices, Vector<int> &p_indices) {