### 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)

DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_BOTTOM_LEFT_SIDE, 2, 3);
				DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_LEFT_SIDE, 1, 2);
				DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_TOP_LEFT_SIDE, 0, 1);
				DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_TOP_RIGHT_SIDE, 5, 0);
				DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_RIGHT_SIDE, 4, 5);
			} else {
				DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_BOTTOM_RIGHT_SIDE, 3, 4);
				DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_BOTTOM_SIDE, 4, 5);
				DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_BOTTOM_LEFT_SIDE, 5, 0);
				DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_TOP_LEFT_SIDE, 0, 1);
				DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_TOP_SIDE, 1, 2);
				DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_TOP_RIGHT_SIDE, 2, 3);
			}
		}
	}
#undef DRAW_SIDE_IF_NEEDED
}
PackedStringArray TileMap::get_configuration_warnings() const {
	PackedStringArray warnings = Node::get_configuration_warnings();
	
	RBSet<int> y_sorted_z_index;
	for (const Ref<TileMapLayer> &layer : layers) {
		if (layer->is_y_sort_enabled()) {
			y_sorted_z_index.insert(layer->get_z_index());
		}
	}
	
	for (const Ref<TileMapLayer> &layer : layers) {
		if (!layer->is_y_sort_enabled() && y_sorted_z_index.has(layer->get_z_index())) {
			warnings.push_back(RTR("A Y-sorted layer has the same Z-index value as a not Y-sorted layer.\nThis may lead to unwanted behaviors, as a layer that is not Y-sorted will be Y-sorted as a whole with tiles from Y-sorted layers."));