### 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)

ClassDB::bind_method(D_METHOD("get_used_rect"), &TileMap::get_used_rect);
	ClassDB::bind_method(D_METHOD("map_to_local", "map_position"), &TileMap::map_to_local);
	ClassDB::bind_method(D_METHOD("local_to_map", "local_position"), &TileMap::local_to_map);
	ClassDB::bind_method(D_METHOD("get_neighbor_cell", "coords", "neighbor"), &TileMap::get_neighbor_cell);
	ClassDB::bind_method(D_METHOD("_update_dirty_quadrants"), &TileMap::_update_dirty_quadrants);
	ClassDB::bind_method(D_METHOD("_tile_set_changed_deferred_update"), &TileMap::_tile_set_changed_deferred_update);
	GDVIRTUAL_BIND(_use_tile_data_runtime_update, "layer", "coords");
	GDVIRTUAL_BIND(_tile_data_runtime_update, "layer", "coords", "tile_data");
	ADD_PROPERTY(PropertyInfo(Variant::OBJECT, "tile_set", PROPERTY_HINT_RESOURCE_TYPE, "TileSet"), "set_tileset", "get_tileset");
	ADD_PROPERTY(PropertyInfo(Variant::INT, "cell_quadrant_size", PROPERTY_HINT_RANGE, "1,128,1"), "set_quadrant_size", "get_quadrant_size");
	ADD_PROPERTY(PropertyInfo(Variant::BOOL, "collision_animatable"), "set_collision_animatable", "is_collision_animatable");
	ADD_PROPERTY(PropertyInfo(Variant::INT, "collision_visibility_mode", PROPERTY_HINT_ENUM, "Default,Force Show,Force Hide"), "set_collision_visibility_mode", "get_collision_visibility_mode");
	ADD_PROPERTY(PropertyInfo(Variant::INT, "navigation_visibility_mode", PROPERTY_HINT_ENUM, "Default,Force Show,Force Hide"), "set_navigation_visibility_mode", "get_navigation_visibility_mode");
	ADD_ARRAY("layers", "layer_");
	ADD_PROPERTY_DEFAULT("format", TileMapLayer::FORMAT_1);
	ADD_SIGNAL(MethodInfo(CoreStringNames::get_singleton()->changed));
	BIND_ENUM_CONSTANT(VISIBILITY_MODE_DEFAULT);
	BIND_ENUM_CONSTANT(VISIBILITY_MODE_FORCE_HIDE);
	BIND_ENUM_CONSTANT(VISIBILITY_MODE_FORCE_SHOW);
}
void TileMap::_tile_set_changed() {
	emit_signal(CoreStringNames::get_singleton()->changed);
	_tile_set_changed_deferred_update_needed = true;
	for (Ref<TileMapLayer> &layer : layers) {
		layer->clear_instantiated_scenes();
	}
	call_deferred(SNAME("_tile_set_changed_deferred_update"));
	update_configuration_warnings();
}
void TileMap::_tile_set_changed_deferred_update() {