### 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)

RenderingServer *rs = RenderingServer::get_singleton();
	if (!canvas_item.is_valid()) {
		RID ci = rs->canvas_item_create();
		rs->canvas_item_set_parent(ci, tile_map_node->get_canvas_item());
		rs->canvas_item_set_draw_index(ci, layer_index_in_tile_map_node - (int64_t)0x80000000);
		canvas_item = ci;
	}
	RID &ci = canvas_item;
	rs->canvas_item_set_sort_children_by_y(ci, y_sort_enabled);
	rs->canvas_item_set_use_parent_material(ci, tile_map_node->get_use_parent_material() || tile_map_node->get_material().is_valid());
	rs->canvas_item_set_z_index(ci, z_index);
	rs->canvas_item_set_default_texture_filter(ci, RS::CanvasItemTextureFilter(tile_map_node->get_texture_filter_in_tree()));
	rs->canvas_item_set_default_texture_repeat(ci, RS::CanvasItemTextureRepeat(tile_map_node->get_texture_repeat_in_tree()));
	rs->canvas_item_set_light_mask(ci, tile_map_node->get_light_mask());
	Color layer_modulate = modulate;
	int selected_layer = tile_map_node->get_selected_layer();
	if (selected_layer >= 0 && layer_index_in_tile_map_node != selected_layer) {
		int z_selected = tile_map_node->get_layer_z_index(selected_layer);
		if (z_index < z_selected || (z_index == z_selected && layer_index_in_tile_map_node < selected_layer)) {
			layer_modulate = layer_modulate.darkened(0.5);
		} else if (z_index > z_selected || (z_index == z_selected && layer_index_in_tile_map_node > selected_layer)) {
			layer_modulate = layer_modulate.darkened(0.5);
			layer_modulate.a *= 0.3;
		}
	}
	rs->canvas_item_set_modulate(ci, layer_modulate);
}
void TileMapLayer::_rendering_cleanup() {