No, that website takes that into account, that's the point. It's just like the federal and state tax. The 10% penalty is a flat fixed amount. Just like the 12% for federal. That's nice the website calculates it out for you. So you don't have to figure it out yourself. Even though the penalty is a fixed 10% of the gross the federal and state withholding amounts are just estimates. The actual income tax will be based on your total income.
Hope that makes sense.
