### 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_V(p_terrain_set < 0 || p_terrain_set >= get_terrain_sets_count(), Vector<Point2>());
	TileSet::TerrainMode terrain_mode = get_terrain_set_mode(p_terrain_set);
	if (tile_shape == TileSet::TILE_SHAPE_SQUARE) {
		if (terrain_mode == TileSet::TERRAIN_MODE_MATCH_CORNERS_AND_SIDES) {
			return _get_square_corner_or_side_terrain_peering_bit_polygon(tile_size, p_bit);
		} else if (terrain_mode == TileSet::TERRAIN_MODE_MATCH_CORNERS) {
			return _get_square_corner_terrain_peering_bit_polygon(tile_size, p_bit);
		} else { 
			return _get_square_side_terrain_peering_bit_polygon(tile_size, p_bit);
		}
	} else if (tile_shape == TileSet::TILE_SHAPE_ISOMETRIC) {
		if (terrain_mode == TileSet::TERRAIN_MODE_MATCH_CORNERS_AND_SIDES) {
			return _get_isometric_corner_or_side_terrain_peering_bit_polygon(tile_size, p_bit);
		} else if (terrain_mode == TileSet::TERRAIN_MODE_MATCH_CORNERS) {
			return _get_isometric_corner_terrain_peering_bit_polygon(tile_size, p_bit);
		} else { 
			return _get_isometric_side_terrain_peering_bit_polygon(tile_size, p_bit);
		}
	} else {
		float overlap = 0.0;
		switch (tile_shape) {
			case TileSet::TILE_SHAPE_HEXAGON: