### 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)

TileMapQuadrant &q = Q->value;
	if (!q.dirty_list_element.in_list()) {
		dirty_quadrant_list.add(&q.dirty_list_element);
	}
	tile_map_node->queue_update_dirty_quadrants();
}
void TileMapLayer::_erase_quadrant(HashMap<Vector2i, TileMapQuadrant>::Iterator Q) {
	
	TileMapQuadrant *q = &(Q->value);
	
	if (tile_map_node->get_tileset().is_valid()) {
		_rendering_cleanup_quadrant(q);
		_physics_cleanup_quadrant(q);
		_navigation_cleanup_quadrant(q);
		_scenes_cleanup_quadrant(q);
	}
	
	if (q->dirty_list_element.in_list()) {
		dirty_quadrant_list.remove(&(q->dirty_list_element));
	}
	
	RenderingServer *rs = RenderingServer::get_singleton();
	rs->free(q->debug_canvas_item);
	quadrant_map.remove(Q);
	rect_cache_dirty = true;
}
void TileMapLayer::_rendering_update() {