### 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 (!show_navigation) {
		return;
	}
#ifdef DEBUG_ENABLED
	RenderingServer *rs = RenderingServer::get_singleton();
	const NavigationServer2D *ns2d = NavigationServer2D::get_singleton();
	bool enabled_geometry_face_random_color = ns2d->get_debug_navigation_enable_geometry_face_random_color();
	bool enabled_edge_lines = ns2d->get_debug_navigation_enable_edge_lines();
	Color debug_face_color = ns2d->get_debug_navigation_geometry_face_color();
	Color debug_edge_color = ns2d->get_debug_navigation_geometry_edge_color();
	RandomPCG rand;
	Vector2 quadrant_pos = tile_map_node->map_to_local(p_quadrant->coords * get_effective_quadrant_size());
	for (const Vector2i &E_cell : p_quadrant->cells) {
		TileMapCell c = get_cell(E_cell, 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) {
				const TileData *tile_data;
				if (p_quadrant->runtime_tile_data_cache.has(E_cell)) {
					tile_data = p_quadrant->runtime_tile_data_cache[E_cell];
				} else {
					tile_data = atlas_source->get_tile_data(c.get_atlas_coords(), c.alternative_tile);
				}
				Transform2D cell_to_quadrant;
				cell_to_quadrant.set_origin(tile_map_node->map_to_local(E_cell) - quadrant_pos);