### 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("set_tileset", "tileset"), &TileMap::set_tileset);
	ClassDB::bind_method(D_METHOD("get_tileset"), &TileMap::get_tileset);
	ClassDB::bind_method(D_METHOD("set_quadrant_size", "size"), &TileMap::set_quadrant_size);
	ClassDB::bind_method(D_METHOD("get_quadrant_size"), &TileMap::get_quadrant_size);
	ClassDB::bind_method(D_METHOD("get_layers_count"), &TileMap::get_layers_count);
	ClassDB::bind_method(D_METHOD("add_layer", "to_position"), &TileMap::add_layer);
	ClassDB::bind_method(D_METHOD("move_layer", "layer", "to_position"), &TileMap::move_layer);
	ClassDB::bind_method(D_METHOD("remove_layer", "layer"), &TileMap::remove_layer);
	ClassDB::bind_method(D_METHOD("set_layer_name", "layer", "name"), &TileMap::set_layer_name);
	ClassDB::bind_method(D_METHOD("get_layer_name", "layer"), &TileMap::get_layer_name);
	ClassDB::bind_method(D_METHOD("set_layer_enabled", "layer", "enabled"), &TileMap::set_layer_enabled);
	ClassDB::bind_method(D_METHOD("is_layer_enabled", "layer"), &TileMap::is_layer_enabled);
	ClassDB::bind_method(D_METHOD("set_layer_modulate", "layer", "modulate"), &TileMap::set_layer_modulate);
	ClassDB::bind_method(D_METHOD("get_layer_modulate", "layer"), &TileMap::get_layer_modulate);
	ClassDB::bind_method(D_METHOD("set_layer_y_sort_enabled", "layer", "y_sort_enabled"), &TileMap::set_layer_y_sort_enabled);
	ClassDB::bind_method(D_METHOD("is_layer_y_sort_enabled", "layer"), &TileMap::is_layer_y_sort_enabled);
	ClassDB::bind_method(D_METHOD("set_layer_y_sort_origin", "layer", "y_sort_origin"), &TileMap::set_layer_y_sort_origin);
	ClassDB::bind_method(D_METHOD("get_layer_y_sort_origin", "layer"), &TileMap::get_layer_y_sort_origin);
	ClassDB::bind_method(D_METHOD("set_layer_z_index", "layer", "z_index"), &TileMap::set_layer_z_index);
	ClassDB::bind_method(D_METHOD("get_layer_z_index", "layer"), &TileMap::get_layer_z_index);
	ClassDB::bind_method(D_METHOD("set_layer_navigation_map", "layer", "map"), &TileMap::set_layer_navigation_map);
	ClassDB::bind_method(D_METHOD("get_layer_navigation_map", "layer"), &TileMap::get_layer_navigation_map);