### 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 (atlas_source) {
					const TileData *tile_data;
					if (q.runtime_tile_data_cache.has(E_cell)) {
						tile_data = q.runtime_tile_data_cache[E_cell];
					} else {
						tile_data = atlas_source->get_tile_data(c.get_atlas_coords(), c.alternative_tile);
					}
					q.navigation_regions[E_cell].resize(tile_set->get_navigation_layers_count());
					for (int navigation_layer_index = 0; navigation_layer_index < tile_set->get_navigation_layers_count(); navigation_layer_index++) {
						Ref<NavigationPolygon> navigation_polygon;
						navigation_polygon = tile_data->get_navigation_polygon(navigation_layer_index);
						if (navigation_polygon.is_valid()) {
							Transform2D tile_transform;
							tile_transform.set_origin(tile_map_node->map_to_local(E_cell));
							RID region = NavigationServer2D::get_singleton()->region_create();
							NavigationServer2D::get_singleton()->region_set_owner_id(region, tile_map_node->get_instance_id());
							NavigationServer2D::get_singleton()->region_set_map(region, navigation_map);
							NavigationServer2D::get_singleton()->region_set_transform(region, tilemap_xform * tile_transform);
							NavigationServer2D::get_singleton()->region_set_navigation_layers(region, tile_set->get_navigation_layer_layers(navigation_layer_index));
							NavigationServer2D::get_singleton()->region_set_navigation_polygon(region, navigation_polygon);
							q.navigation_regions[E_cell].write[navigation_layer_index] = region;
						}
					}
				}
			}
		}
		q_list_element = q_list_element->next();
	}
}
void TileMapLayer::_navigation_update() {