### 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)

RBSet<Vector2i> painted_set;
	for (int i = p_coords_array.size() - 1; i >= 0; i--) {
		const Vector2i &coords = p_coords_array[i];
		can_modify_list.push_back(coords);
		can_modify_set.insert(coords);
		painted_set.insert(coords);
	}
	for (Vector2i coords : p_coords_array) {
		
		for (int j = 0; j < TileSet::CELL_NEIGHBOR_MAX; j++) {
			TileSet::CellNeighbor bit = TileSet::CellNeighbor(j);
			if (tile_set->is_valid_terrain_peering_bit(p_terrain_set, bit)) {
				Vector2i neighbor = tile_map_node->get_neighbor_cell(coords, bit);
				if (!can_modify_set.has(neighbor)) {
					can_modify_list.push_back(neighbor);
					can_modify_set.insert(neighbor);
				}
			}
		}
	}
	RBSet<TerrainConstraint> constraints;
	
	for (Vector2i coords : p_coords_array) {
		
		TerrainConstraint c = TerrainConstraint(tile_map_node, coords, p_terrain);
		c.set_priority(10);
		constraints.insert(c);
	}
	for (int i = 0; i < p_coords_array.size() - 1; i++) {