### 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)

Error err = ConvexHullComputer::convex_hull(varr, md);
						if (err == OK) {
							PackedVector3Array faces;
							for (const Geometry3D::MeshData::Face &face : md.faces) {
								for (uint32_t k = 2; k < face.indices.size(); ++k) {
									faces.push_back(md.vertices[face.indices[0]]);
									faces.push_back(md.vertices[face.indices[k - 1]]);
									faces.push_back(md.vertices[face.indices[k]]);
								}
							}
							_add_faces(faces, transform, p_vertices, p_indices);
						}
					}
					HeightMapShape3D *heightmap_shape = Object::cast_to<HeightMapShape3D>(*s);
					if (heightmap_shape) {
						int heightmap_depth = heightmap_shape->get_map_depth();
						int heightmap_width = heightmap_shape->get_map_width();
						if (heightmap_depth >= 2 && heightmap_width >= 2) {
							const Vector<real_t> &map_data = heightmap_shape->get_map_data();
							Vector2 heightmap_gridsize(heightmap_width - 1, heightmap_depth - 1);
							Vector2 start = heightmap_gridsize * -0.5;
							Vector<Vector3> vertex_array;
							vertex_array.resize((heightmap_depth - 1) * (heightmap_width - 1) * 6);
							int map_data_current_index = 0;
							for (int d = 0; d < heightmap_depth; d++) {
								for (int w = 0; w < heightmap_width; w++) {
									if (map_data_current_index + 1 + heightmap_depth < map_data.size()) {
										float top_left_height = map_data[map_data_current_index];
										float top_right_height = map_data[map_data_current_index + 1];
										float bottom_left_height = map_data[map_data_current_index + heightmap_depth];