### 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)

break;
		}
	}
	
	if (!is_y_sort_enabled()) {
		for (const Ref<TileMapLayer> &layer : layers) {
			if (layer->is_y_sort_enabled()) {
				warnings.push_back(RTR("A TileMap layer is set as Y-sorted, but Y-sort is not enabled on the TileMap node itself."));
				break;
			}
		}
	}
	
	if (tile_set.is_valid() && tile_set->get_tile_shape() == TileSet::TILE_SHAPE_ISOMETRIC) {
		bool warn = !is_y_sort_enabled();
		if (!warn) {
			for (const Ref<TileMapLayer> &layer : layers) {
				if (!layer->is_y_sort_enabled()) {
					warn = true;
					break;
				}
			}
		}
		if (warn) {
			warnings.push_back(RTR("Isometric TileSet will likely not look as intended without Y-sort enabled for the TileMap and all of its layers."));
		}
	}
	return warnings;
}
void TileMap::_bind_methods() {