### 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)

ClassDB::bind_method(D_METHOD("is_target_reachable"), &NavigationAgent3D::is_target_reachable);
	ClassDB::bind_method(D_METHOD("is_navigation_finished"), &NavigationAgent3D::is_navigation_finished);
	ClassDB::bind_method(D_METHOD("get_final_position"), &NavigationAgent3D::get_final_position);
	ClassDB::bind_method(D_METHOD("_avoidance_done", "new_velocity"), &NavigationAgent3D::_avoidance_done);
	ClassDB::bind_method(D_METHOD("set_avoidance_layers", "layers"), &NavigationAgent3D::set_avoidance_layers);
	ClassDB::bind_method(D_METHOD("get_avoidance_layers"), &NavigationAgent3D::get_avoidance_layers);
	ClassDB::bind_method(D_METHOD("set_avoidance_mask", "mask"), &NavigationAgent3D::set_avoidance_mask);
	ClassDB::bind_method(D_METHOD("get_avoidance_mask"), &NavigationAgent3D::get_avoidance_mask);
	ClassDB::bind_method(D_METHOD("set_avoidance_layer_value", "layer_number", "value"), &NavigationAgent3D::set_avoidance_layer_value);
	ClassDB::bind_method(D_METHOD("get_avoidance_layer_value", "layer_number"), &NavigationAgent3D::get_avoidance_layer_value);
	ClassDB::bind_method(D_METHOD("set_avoidance_mask_value", "mask_number", "value"), &NavigationAgent3D::set_avoidance_mask_value);
	ClassDB::bind_method(D_METHOD("get_avoidance_mask_value", "mask_number"), &NavigationAgent3D::get_avoidance_mask_value);
	ClassDB::bind_method(D_METHOD("set_avoidance_priority", "priority"), &NavigationAgent3D::set_avoidance_priority);
	ClassDB::bind_method(D_METHOD("get_avoidance_priority"), &NavigationAgent3D::get_avoidance_priority);
	ADD_GROUP("Pathfinding", "");
	ADD_PROPERTY(PropertyInfo(Variant::VECTOR3, "target_position", PROPERTY_HINT_NONE, "", PROPERTY_USAGE_NO_EDITOR), "set_target_position", "get_target_position");
	ADD_PROPERTY(PropertyInfo(Variant::FLOAT, "path_desired_distance", PROPERTY_HINT_RANGE, "0.1,100,0.01,or_greater,suffix:m"), "set_path_desired_distance", "get_path_desired_distance");
	ADD_PROPERTY(PropertyInfo(Variant::FLOAT, "target_desired_distance", PROPERTY_HINT_RANGE, "0.1,100,0.01,or_greater,suffix:m"), "set_target_desired_distance", "get_target_desired_distance");
	ADD_PROPERTY(PropertyInfo(Variant::FLOAT, "path_height_offset", PROPERTY_HINT_RANGE, "-100.0,100,0.01,or_greater,suffix:m"), "set_path_height_offset", "get_path_height_offset");
	ADD_PROPERTY(PropertyInfo(Variant::FLOAT, "path_max_distance", PROPERTY_HINT_RANGE, "0.01,100,0.1,or_greater,suffix:m"), "set_path_max_distance", "get_path_max_distance");
	ADD_PROPERTY(PropertyInfo(Variant::INT, "navigation_layers", PROPERTY_HINT_LAYERS_3D_NAVIGATION), "set_navigation_layers", "get_navigation_layers");
	ADD_PROPERTY(PropertyInfo(Variant::INT, "pathfinding_algorithm", PROPERTY_HINT_ENUM, "AStar"), "set_pathfinding_algorithm", "get_pathfinding_algorithm");
	ADD_PROPERTY(PropertyInfo(Variant::INT, "path_postprocessing", PROPERTY_HINT_ENUM, "Corridorfunnel,Edgecentered"), "set_path_postprocessing", "get_path_postprocessing");
	ADD_PROPERTY(PropertyInfo(Variant::INT, "path_metadata_flags", PROPERTY_HINT_FLAGS, "Include Types,Include RIDs,Include Owners"), "set_path_metadata_flags", "get_path_metadata_flags");
	ADD_GROUP("Avoidance", "");
	ADD_PROPERTY(PropertyInfo(Variant::BOOL, "avoidance_enabled"), "set_avoidance_enabled", "get_avoidance_enabled");
	ADD_PROPERTY(PropertyInfo(Variant::VECTOR3, "velocity", PROPERTY_HINT_NONE, "", PROPERTY_USAGE_NO_EDITOR), "set_velocity", "get_velocity");
	ADD_PROPERTY(PropertyInfo(Variant::FLOAT, "height", PROPERTY_HINT_RANGE, "0.01,100,0.01,or_greater,suffix:m"), "set_height", "get_height");
	ADD_PROPERTY(PropertyInfo(Variant::FLOAT, "radius", PROPERTY_HINT_RANGE, "0.01,100,0.01,or_greater,suffix:m"), "set_radius", "get_radius");
	ADD_PROPERTY(PropertyInfo(Variant::FLOAT, "neighbor_distance", PROPERTY_HINT_RANGE, "0.1,10000,0.01,or_greater,suffix:m"), "set_neighbor_distance", "get_neighbor_distance");