### Godot version

v4.1.rc1.mono.official [1f9e540f1]

### System information

Godot v4.1.rc1.mono - Windows 10.0.19045 - Vulkan (Forward+) - dedicated NVIDIA GeForce GTX 1660 Ti with Max-Q Design (NVIDIA; 31.0.15.3179) - Intel(R) Core(TM) i7-9750H CPU @ 2.60GHz (12 Threads)

### Issue description

When NavigationAgent3D is instantiated at runtime and added to the scene tree, invisible/impassable obstacle is added at the global origin position (0, 0, 0).

### Steps to reproduce

1. Run attached MRP
2. Click with `left mouse button` at the world origin to make agent walk
3. Click `space` on your keyboard to instantiate NavigationAgent3D
4. Click left mouse button to walk through world origin position again
5. Player gets stuck on obstacle at the world origin position

https://github.com/godotengine/godot/assets/8630984/fc9b32fb-25cb-46d6-9a98-ff299e2c0b1c



### Minimal reproduction project

[MRP.zip](https://github.com/godotengine/godot/files/11910363/MRP.zip)

case NOTIFICATION_PARENTED: {
			if (is_inside_tree() && (get_parent() != agent_parent)) {
				
				
				
				
				set_agent_parent(get_parent());
				set_physics_process_internal(true);
			}
		} break;
		case NOTIFICATION_UNPARENTED: {
			
			set_agent_parent(nullptr);
			set_physics_process_internal(false);
		} break;
		case NOTIFICATION_EXIT_TREE: {
			set_agent_parent(nullptr);
			set_physics_process_internal(false);
#ifdef DEBUG_ENABLED
			if (debug_path_instance.is_valid()) {
				RenderingServer::get_singleton()->canvas_item_set_visible(debug_path_instance, false);
			}
#endif 
		} break;
		case NOTIFICATION_PAUSED: {
			if (agent_parent) {
				NavigationServer2D::get_singleton()->agent_set_paused(get_rid(), !agent_parent->can_process());
			}
		} break;
		case NOTIFICATION_UNPAUSED: {