### 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)

ERR_FAIL_INDEX(p_layer, (int)layers.size());
	ERR_FAIL_INDEX(p_to_pos, (int)layers.size() + 1);
	
	_clear_internals();
	Ref<TileMapLayer> layer = layers[p_layer];
	layers.insert(p_to_pos, layer);
	layers.remove_at(p_to_pos < p_layer ? p_layer + 1 : p_layer);
	for (unsigned int i = 0; i < layers.size(); i++) {
		layers[i]->set_layer_index_in_tile_map_node(i);
	}
	_recreate_internals();
	notify_property_list_changed();
	if (selected_layer == p_layer) {
		selected_layer = p_to_pos < p_layer ? p_to_pos - 1 : p_to_pos;
	}
	emit_signal(CoreStringNames::get_singleton()->changed);
	update_configuration_warnings();
}
void TileMap::remove_layer(int p_layer) {