### 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)

TileData *tile_data = atlas_source->get_tile_data(cell.get_atlas_coords(), cell.alternative_tile);
				if (tile_data && tile_data->get_terrain_set() == p_terrain_set) {
					current_pattern = tile_data->get_terrains_pattern();
				}
			}
		}
		TileSet::TerrainsPattern pattern = _get_best_terrain_pattern_for_constraints(p_terrain_set, coords, constraints, current_pattern);
		
		RBSet<TerrainConstraint> new_constraints = _get_terrain_constraints_from_added_pattern(coords, p_terrain_set, pattern);
		for (const TerrainConstraint &E_constraint : new_constraints) {
			if (constraints.has(E_constraint)) {
				constraints.erase(E_constraint);
			}
			TerrainConstraint c = E_constraint;
			c.set_priority(5);
			constraints.insert(c);
		}
		output[coords] = pattern;
	}
	return output;
}
HashMap<Vector2i, TileSet::TerrainsPattern> TileMapLayer::terrain_fill_connect(const Vector<Vector2i> &p_coords_array, int p_terrain_set, int p_terrain, bool p_ignore_empty_terrains) {
	HashMap<Vector2i, TileSet::TerrainsPattern> output;
	const Ref<TileSet> &tile_set = tile_map_node->get_tileset();
	ERR_FAIL_COND_V(!tile_set.is_valid(), output);
	ERR_FAIL_INDEX_V(p_terrain_set, tile_set->get_terrain_sets_count(), output);
	
	Vector<Vector2i> can_modify_list;
	RBSet<Vector2i> can_modify_set;