### 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)

}
	if (!show_collision) {
		return;
	}
	RenderingServer *rs = RenderingServer::get_singleton();
	PhysicsServer2D *ps = PhysicsServer2D::get_singleton();
	Color debug_collision_color = tile_map_node->get_tree()->get_debug_collisions_color();
	Vector<Color> color;
	color.push_back(debug_collision_color);
	Vector2 quadrant_pos = tile_map_node->map_to_local(p_quadrant->coords * get_effective_quadrant_size());
	Transform2D quadrant_to_local;
	quadrant_to_local.set_origin(quadrant_pos);
	Transform2D global_to_quadrant = (tile_map_node->get_global_transform() * quadrant_to_local).affine_inverse();
	for (RID body : p_quadrant->bodies) {
		Transform2D body_to_quadrant = global_to_quadrant * Transform2D(ps->body_get_state(body, PhysicsServer2D::BODY_STATE_TRANSFORM));
		rs->canvas_item_add_set_transform(p_quadrant->debug_canvas_item, body_to_quadrant);
		for (int shape_index = 0; shape_index < ps->body_get_shape_count(body); shape_index++) {
			const RID &shape = ps->body_get_shape(body, shape_index);
			PhysicsServer2D::ShapeType type = ps->shape_get_type(shape);
			if (type == PhysicsServer2D::SHAPE_CONVEX_POLYGON) {
				Vector<Vector2> polygon = ps->shape_get_data(shape);
				rs->canvas_item_add_polygon(p_quadrant->debug_canvas_item, polygon, color);
			} else {
				WARN_PRINT("Wrong shape type for a tile, should be SHAPE_CONVEX_POLYGON.");
			}
		}
		rs->canvas_item_add_set_transform(p_quadrant->debug_canvas_item, Transform2D());
	}
};
void TileMapLayer::_navigation_update_dirty_quadrants(SelfList<TileMapQuadrant>::List &r_dirty_quadrant_list) {