### 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 (!tile_map_node->GDVIRTUAL_IS_OVERRIDDEN(_use_tile_data_runtime_update) || !tile_map_node->GDVIRTUAL_IS_OVERRIDDEN(_tile_data_runtime_update)) {
		return;
	}
	const Ref<TileSet> &tile_set = tile_map_node->get_tileset();
	SelfList<TileMapQuadrant> *q_list_element = r_dirty_quadrant_list.first();
	while (q_list_element) {
		TileMapQuadrant &q = *q_list_element->self();
		
		for (const KeyValue<Vector2, Vector2i> &E_cell : q.local_to_map) {
			TileMapCell c = get_cell(E_cell.value, true);
			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;
				}
				TileSetAtlasSource *atlas_source = Object::cast_to<TileSetAtlasSource>(source);
				if (atlas_source) {
					bool ret = false;
					if (tile_map_node->GDVIRTUAL_CALL(_use_tile_data_runtime_update, layer_index_in_tile_map_node, E_cell.value, ret) && ret) {
						TileData *tile_data = atlas_source->get_tile_data(c.get_atlas_coords(), c.alternative_tile);
						
						TileData *tile_data_runtime_use = tile_data->duplicate();
						tile_data_runtime_use->set_allow_transform(true);
						q.runtime_tile_data_cache[E_cell.value] = tile_data_runtime_use;
						tile_map_node->GDVIRTUAL_CALL(_tile_data_runtime_update, layer_index_in_tile_map_node, E_cell.value, tile_data_runtime_use);
					}
				}
			}