### 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)
polygon.push_back(Vector2(0, -1) * unit);
			break;
		default:
			break;
	}
	return polygon;
}
Vector<Point2> TileSet::_get_half_offset_terrain_polygon(Vector2i p_size, float p_overlap, TileSet::TileOffsetAxis p_offset_axis) {
	Vector2 unit = Vector2(p_size) / 6.0;
	if (p_offset_axis == TileSet::TILE_OFFSET_AXIS_HORIZONTAL) {
		return {
			Vector2(1, 1.0 - p_overlap * 2.0) * unit,
			Vector2(0, 1) * unit,
			Vector2(-1, 1.0 - p_overlap * 2.0) * unit,
			Vector2(-1, -1.0 + p_overlap * 2.0) * unit,
			Vector2(0, -1) * unit,
			Vector2(1, -1.0 + p_overlap * 2.0) * unit,
		};
	} else {
		return {
			Vector2(1, 0) * unit,
			Vector2(1.0 - p_overlap * 2.0, -1) * unit,
			Vector2(-1.0 + p_overlap * 2.0, -1) * unit,
			Vector2(-1, 0) * unit,
			Vector2(-1.0 + p_overlap * 2.0, 1) * unit,
			Vector2(1.0 - p_overlap * 2.0, 1) * unit,
		};
	}
}
Vector<Point2> TileSet::_get_half_offset_corner_or_side_terrain_peering_bit_polygon(Vector2i p_size, float p_overlap, TileSet::TileOffsetAxis p_offset_axis, TileSet::CellNeighbor p_bit) {