### Godot version

4.2.dev3.official[013e8e3af]

### System information

Godot v4.2.dev3 - Arch Linux #1 SMP PREEMPT_DYNAMIC Fri, 11 Aug 2023 11:03:36 +0000 - X11 - GLES3 (Compatibility) - NVIDIA GeForce RTX 2060 (nvidia; 535.98) - Intel(R) Core(TM) i7-10875H CPU @ 2.30GHz (16 Threads)

### Issue description

`TileMap.get_used_cells_by_id()` seems not work as expected.
It seems that this method will return the same result as "TileMap.get_used_cells()" since Godot 4.2dev2.
The arguments  (`source_id: int`, `atlas_coords: Vector2i`, `alternative_tile: int`) of `get_used_cells_by_id()` seems not make the filter working as expected.  It would only return the same result as `get_used_cells()`, contains all the tiles on the layer.

### Steps to reproduce

1. create a tilemap scene
2. attach a tileset, that contains  at least 2 tiles , paint some tiles.
3. calls Tilemap.get_used_cells_by_id(layer, source_id, atlas_coords,alternative_tile)
4. run it

### Minimal reproduction project

run tile_map.tscn by Godot4dev3 (or custom build)
[tilemap_debug.zip](https://github.com/godotengine/godot/files/12369631/tilemap_debug.zip)

TileSetSource *source;
			if (tile_set->has_source(c.source_id)) {
				source = *tile_set->get_source(c.source_id);
				if (!source->has_tile(c.get_atlas_coords()) || !source->has_alternative_tile(c.get_atlas_coords(), c.alternative_tile)) {
					continue;
				}
				TileSetScenesCollectionSource *scenes_collection_source = Object::cast_to<TileSetScenesCollectionSource>(source);
				if (scenes_collection_source) {
					Ref<PackedScene> packed_scene = scenes_collection_source->get_scene_tile_scene(c.alternative_tile);
					if (packed_scene.is_valid()) {
						Node *scene = packed_scene->instantiate();
						Control *scene_as_control = Object::cast_to<Control>(scene);
						Node2D *scene_as_node2d = Object::cast_to<Node2D>(scene);
						if (scene_as_control) {
							scene_as_control->set_position(tile_map_node->map_to_local(E_cell) + scene_as_control->get_position());
						} else if (scene_as_node2d) {
							Transform2D xform;
							xform.set_origin(tile_map_node->map_to_local(E_cell));
							scene_as_node2d->set_transform(xform * scene_as_node2d->get_transform());
						}
						tile_map_node->add_child(scene);
						q.scenes[E_cell] = scene->get_name();
					}
				}
			}
		}
		q_list_element = q_list_element->next();
	}
}
void TileMapLayer::_scenes_cleanup_quadrant(TileMapQuadrant *p_quadrant) {