If at the end of the year, you owe more than $1,000 you will be subject to a penalty unless you qualify for a safe harbor exception. The penalty is currently computed using 3% per year or .25% per month.
You don’t get penalized for not paying your taxes in advance, estimated taxes, etc.. You only get penalized when you don’t pay. When you have withholding done all your doing is giving the Government a no interest loan on your money.
Turns out they were going to charge a service fee of $160. So I canceled the transaction and mailed in a check. I had to chuckle when I saw a message there urging people to go paperless.