### 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 (p_callback.is_valid()) {
		Callable::CallError ce;
		Variant result;
		p_callback.callp(nullptr, 0, result, ce);
		if (ce.error == Callable::CallError::CALL_OK) {
			
		}
	}
}
void NavigationMeshGenerator::bake_from_source_geometry_data(Ref<NavigationMesh> p_navigation_mesh, const Ref<NavigationMeshSourceGeometryData3D> &p_source_geometry_data, const Callable &p_callback) {
	ERR_FAIL_COND_MSG(!p_navigation_mesh.is_valid(), "Invalid navigation mesh.");
	ERR_FAIL_COND_MSG(!p_source_geometry_data.is_valid(), "Invalid NavigationMeshSourceGeometryData3D.");
	ERR_FAIL_COND_MSG(!p_source_geometry_data->has_data(), "NavigationMeshSourceGeometryData3D is empty. Parse source geometry first.");
	generator_mutex.lock();
	if (baking_navmeshes.has(p_navigation_mesh)) {
		generator_mutex.unlock();
		ERR_FAIL_MSG("NavigationMesh is already baking. Wait for current bake to finish.");
	} else {
		baking_navmeshes.insert(p_navigation_mesh);
		generator_mutex.unlock();
	}
#ifndef _3D_DISABLED
	const Vector<float> vertices = p_source_geometry_data->get_vertices();
	const Vector<int> indices = p_source_geometry_data->get_indices();
	if (vertices.size() < 3 || indices.size() < 3) {
		return;
	}
	rcHeightfield *hf = nullptr;
	rcCompactHeightfield *chf = nullptr;
	rcContourSet *cset = nullptr;