### 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)

ERR_PRINT(vformat("No valid tile in Tileset for: tile:%s coords:%s flip_h:%s flip_v:%s transpose:%s", v, Vector2i(coord_x, coord_y), flip_h, flip_v, transpose));
				}
			} else {
				int compatibility_alternative_tile = ((int)flip_h) + ((int)flip_v << 1) + ((int)transpose << 2);
				set_cell(Vector2i(x, y), v, Vector2i(coord_x, coord_y), compatibility_alternative_tile);
			}
#endif
		}
	}
}
Vector<int> TileMapLayer::get_tile_data() const {
	
	Vector<int> tile_data;
	tile_data.resize(tile_map.size() * 3);
	int *w = tile_data.ptrw();
	
	int idx = 0;
	for (const KeyValue<Vector2i, TileMapCell> &E : tile_map) {
		uint8_t *ptr = (uint8_t *)&w[idx];
		encode_uint16((int16_t)(E.key.x), &ptr[0]);
		encode_uint16((int16_t)(E.key.y), &ptr[2]);
		encode_uint16(E.value.source_id, &ptr[4]);
		encode_uint16(E.value.coord_x, &ptr[6]);
		encode_uint16(E.value.coord_y, &ptr[8]);
		encode_uint16(E.value.alternative_tile, &ptr[10]);
		idx += 3;
	}
	return tile_data;
}
void TileMapLayer::clear_instantiated_scenes() {