X2 on flanging , it will stiffen the roof around the hole and then I'd drop in replacement metal from the top. Trim replacement to drop in tight. like said ,little spot welds 6 inch apart, second trip around the panel put spot next to the first and so on . Go easy grinding welds down to keep heat down. Use quality fillers/primer etc and it shouldn't reveal later. Ideally the skin would be the way to go.