### 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)

p_navigation_mesh->add_polygon(nav_indices);
		}
	}
	bake_state = "Cleanup..."; 
	rcFreePolyMesh(poly_mesh);
	poly_mesh = nullptr;
	rcFreePolyMeshDetail(detail_mesh);
	detail_mesh = nullptr;
	bake_state = "Baking finished."; 
#endif 
	generator_mutex.lock();
	baking_navmeshes.erase(p_navigation_mesh);
	generator_mutex.unlock();
	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::_bind_methods() {
	ClassDB::bind_method(D_METHOD("bake", "navigation_mesh", "root_node"), &NavigationMeshGenerator::bake);
	ClassDB::bind_method(D_METHOD("clear", "navigation_mesh"), &NavigationMeshGenerator::clear);
	ClassDB::bind_method(D_METHOD("parse_source_geometry_data", "navigation_mesh", "source_geometry_data", "root_node", "callback"), &NavigationMeshGenerator::parse_source_geometry_data, DEFVAL(Callable()));
	ClassDB::bind_method(D_METHOD("bake_from_source_geometry_data", "navigation_mesh", "source_geometry_data", "callback"), &NavigationMeshGenerator::bake_from_source_geometry_data, DEFVAL(Callable()));
}
#endif