### 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)

real_t radius = dict["radius"];
						real_t height = dict["height"];
						Array arr;
						arr.resize(RS::ARRAY_MAX);
						CapsuleMesh::create_mesh_array(arr, radius, height);
						_add_mesh_array(arr, shapes[i], p_vertices, p_indices);
					} break;
					case PhysicsServer3D::SHAPE_CYLINDER: {
						Dictionary dict = data;
						real_t radius = dict["radius"];
						real_t height = dict["height"];
						Array arr;
						arr.resize(RS::ARRAY_MAX);
						CylinderMesh::create_mesh_array(arr, radius, radius, height);
						_add_mesh_array(arr, shapes[i], p_vertices, p_indices);
					} break;
					case PhysicsServer3D::SHAPE_CONVEX_POLYGON: {
						PackedVector3Array vertices = data;
						Geometry3D::MeshData md;
						Error err = ConvexHullComputer::convex_hull(vertices, 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, shapes[i], p_vertices, p_indices);