### 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)

_scenes_update_dirty_quadrants(dirty_quadrant_list);
	
	RenderingServer *rs = RenderingServer::get_singleton();
	for (SelfList<TileMapQuadrant> *q = dirty_quadrant_list.first(); q; q = q->next()) {
		rs->canvas_item_clear(q->self()->debug_canvas_item);
		Transform2D xform;
		xform.set_origin(tile_map_node->map_to_local(q->self()->coords * get_effective_quadrant_size()));
		rs->canvas_item_set_transform(q->self()->debug_canvas_item, xform);
		_rendering_draw_quadrant_debug(q->self());
		_physics_draw_quadrant_debug(q->self());
		_navigation_draw_quadrant_debug(q->self());
		_scenes_draw_quadrant_debug(q->self());
	}
	
	while (dirty_quadrant_list.first()) {
		
		for (const KeyValue<Vector2i, TileData *> &kv : dirty_quadrant_list.first()->self()->runtime_tile_data_cache) {
			memdelete(kv.value);
		}
		dirty_quadrant_list.remove(dirty_quadrant_list.first());
	}
}
void TileMapLayer::set_cell(const Vector2i &p_coords, int p_source_id, const Vector2i p_atlas_coords, int p_alternative_tile) {
	
	Vector2i pk(p_coords);
	HashMap<Vector2i, TileMapCell>::Iterator E = tile_map.find(pk);
	int source_id = p_source_id;
	Vector2i atlas_coords = p_atlas_coords;
	int alternative_tile = p_alternative_tile;
	if ((source_id == TileSet::INVALID_SOURCE || atlas_coords == TileSetSource::INVALID_ATLAS_COORDS || alternative_tile == TileSetSource::INVALID_TILE_ALTERNATIVE) &&