### 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)

ps->body_set_param(body, PhysicsServer2D::BODY_PARAM_BOUNCE, 0);
							ps->body_set_param(body, PhysicsServer2D::BODY_PARAM_FRICTION, 1);
						} else {
							ps->body_set_param(body, PhysicsServer2D::BODY_PARAM_BOUNCE, physics_material->computed_bounce());
							ps->body_set_param(body, PhysicsServer2D::BODY_PARAM_FRICTION, physics_material->computed_friction());
						}
						q.bodies.push_back(body);
						
						int body_shape_index = 0;
						for (int polygon_index = 0; polygon_index < tile_data->get_collision_polygons_count(tile_set_physics_layer); polygon_index++) {
							
							bool one_way_collision = tile_data->is_collision_polygon_one_way(tile_set_physics_layer, polygon_index);
							float one_way_collision_margin = tile_data->get_collision_polygon_one_way_margin(tile_set_physics_layer, polygon_index);
							int shapes_count = tile_data->get_collision_polygon_shapes_count(tile_set_physics_layer, polygon_index);
							for (int shape_index = 0; shape_index < shapes_count; shape_index++) {
								
								Ref<ConvexPolygonShape2D> shape = tile_data->get_collision_polygon_shape(tile_set_physics_layer, polygon_index, shape_index);
								ps->body_add_shape(body, shape->get_rid());
								ps->body_set_shape_as_one_way_collision(body, body_shape_index, one_way_collision, one_way_collision_margin);
								body_shape_index++;
							}
						}
					}
				}
			}
		}
		q_list_element = q_list_element->next();
	}
}
void TileMapLayer::_physics_cleanup_quadrant(TileMapQuadrant *p_quadrant) {