### 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)

ERR_FAIL_COND_MSG(p_height < 0.0, "Height must be positive.");
	if (Math::is_equal_approx(height, p_height)) {
		return;
	}
	height = p_height;
	NavigationServer3D::get_singleton()->agent_set_height(agent, height);
}
void NavigationAgent3D::set_path_height_offset(real_t p_path_height_offset) {
	path_height_offset = p_path_height_offset;
}
void NavigationAgent3D::set_use_3d_avoidance(bool p_use_3d_avoidance) {
	use_3d_avoidance = p_use_3d_avoidance;
	NavigationServer3D::get_singleton()->agent_set_use_3d_avoidance(agent, use_3d_avoidance);
	notify_property_list_changed();
}
void NavigationAgent3D::set_neighbor_distance(real_t p_distance) {
	if (Math::is_equal_approx(neighbor_distance, p_distance)) {
		return;
	}
	neighbor_distance = p_distance;
	NavigationServer3D::get_singleton()->agent_set_neighbor_distance(agent, neighbor_distance);
}
void NavigationAgent3D::set_max_neighbors(int p_count) {
	if (max_neighbors == p_count) {
		return;
	}
	max_neighbors = p_count;
	NavigationServer3D::get_singleton()->agent_set_max_neighbors(agent, max_neighbors);
}
void NavigationAgent3D::set_time_horizon_agents(real_t p_time_horizon) {