### 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)

for (HashMap<Vector2i, TileMapQuadrant>::Iterator F = quadrant_map.begin(); F; ++F) {
		TileMapQuadrant &q = F->value;
		for (const RID &ci : q.canvas_items) {
			RenderingServer::get_singleton()->canvas_item_set_default_texture_repeat(ci, RS::CanvasItemTextureRepeat(tile_map_node->get_texture_repeat_in_tree()));
			_make_quadrant_dirty(F);
		}
	}
	_rendering_update();
}
void TileMapLayer::update_dirty_quadrants() {
	
	for (SelfList<TileMapQuadrant> *q = dirty_quadrant_list.first(); q; q = q->next()) {
		q->self()->map_to_local.clear();
		q->self()->local_to_map.clear();
		for (const Vector2i &E : q->self()->cells) {
			Vector2i pk = E;
			Vector2 pk_local_coords = tile_map_node->map_to_local(pk);
			q->self()->map_to_local[pk] = pk_local_coords;
			q->self()->local_to_map[pk_local_coords] = pk;
		}
	}
	
	_build_runtime_update_tile_data(dirty_quadrant_list);
	
	_rendering_update_dirty_quadrants(dirty_quadrant_list);
	_physics_update_dirty_quadrants(dirty_quadrant_list);
	_navigation_update_dirty_quadrants(dirty_quadrant_list);