### Godot version

4.2 beta 2

### System information

Pop Os 22.04 lts 12th Gen Intel® Core™ i7-12700H × 20 NVIDIA RTX A2000 8GB 32.0  ram. Tested on Forward+ and Mobile

### Issue description

When painting a tile that is rotated or flipped, it looses its physics layer as demonstrated in this video:  

https://github.com/godotengine/godot/assets/33091666/c10f7325-838f-4112-b90d-0c3d9797d08f

Even though in the video I showed this only happening with one of the tiles, it happens with both of them as long as you rotate or flip it. 

### Steps to reproduce

1. Create a tilemap and a tileset
2. Create a physics layer and set collision_visibility_mode to force show. 
3. Assign just created physics layer to tiles
4. Paint the tiles and use rotate or flip tool. 

### Minimal reproduction project

[TileTest.zip](https://github.com/godotengine/godot/files/13067412/TileTest.zip)
ERR_FAIL_COND(p_terrain_set < 0);
	for (int i = 0; i < TileSet::CELL_NEIGHBOR_MAX; i++) {
		is_valid_bit[i] = (p_tile_set->is_valid_terrain_peering_bit(p_terrain_set, TileSet::CellNeighbor(i)));
		bits[i] = -1;
	}
	valid = true;
}
const int TileSet::INVALID_SOURCE = -1;
const char *TileSet::CELL_NEIGHBOR_ENUM_TO_TEXT[] = {
	PNAME("right_side"),
	PNAME("right_corner"),
	PNAME("bottom_right_side"),
	PNAME("bottom_right_corner"),
	PNAME("bottom_side"),
	PNAME("bottom_corner"),
	PNAME("bottom_left_side"),
	PNAME("bottom_left_corner"),
	PNAME("left_side"),
	PNAME("left_corner"),
	PNAME("top_left_side"),
	PNAME("top_left_corner"),
	PNAME("top_side"),
	PNAME("top_corner"),
	PNAME("top_right_side"),
	PNAME("top_right_corner"),
};
void TileSet::set_tile_shape(TileSet::TileShape p_shape) {