The penalty is calculated on the entire amount you are under-withheld. The $1000 rule is just a "grace period" where they won't calculate it if you come close enough. But if you don't come close enough, the entire under-withholding is penalized.
Note that the penalty plus interest is about 1% per month, spaced out over 4 quarters. So if you owed $1000, that means you under paid by $250 in April, $250 in June, $250 in Sept and $250 on January 15, 2025. So the penalty should be $25 (10% of the April missed payment) plus $17 (7% of the missed payment from June), plus $10 (4% of the missed payment from Sept) plus $5 (2% of the missed payment from January), so $57. Is that close?
And lastly, I would not agree to Turbotax's offer to include a penalty. Leave it off if you can, and wait and see if the IRS bills you. The penalty calculation is only an approximation, so even if you pay it, you may get a bill for a couple extra dollars. If you wait for a bill, they might not penalize you at all, and if they do and it is your first time, you can apply for a waiver.
