### 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)

Ref<Material> mat = tile_data->get_material();
					int tile_z_index = tile_data->get_z_index();
					
					Vector2 tile_position = tile_map_node->map_to_local(q.coords * get_effective_quadrant_size());
					if (tile_map_node->is_y_sort_enabled() && y_sort_enabled) {
						
						tile_position.y += y_sort_origin + tile_data->get_y_sort_origin();
					}
					
					
					RID ci;
					
					if (prev_ci == RID() || prev_material != mat || prev_z_index != tile_z_index) {
						
						ci = rs->canvas_item_create();
						if (mat.is_valid()) {
							rs->canvas_item_set_material(ci, mat->get_rid());
						}
						rs->canvas_item_set_parent(ci, canvas_item);
						rs->canvas_item_set_use_parent_material(ci, tile_map_node->get_use_parent_material() || tile_map_node->get_material().is_valid());
						Transform2D xform;
						xform.set_origin(tile_position);
						rs->canvas_item_set_transform(ci, xform);
						rs->canvas_item_set_light_mask(ci, tile_map_node->get_light_mask());
						rs->canvas_item_set_z_as_relative_to_parent(ci, true);
						rs->canvas_item_set_z_index(ci, tile_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()));
						q.canvas_items.push_back(ci);
						prev_ci = ci;