When you pay with your extension, you are paying off part of your taxes. Not just promising to pay, but paying.
So if your taxes owed for 2018 is $20,200 and you paid $20,000 with your extension, TurboTax "remembers" that and deducts the $20K from the total owed amount, thus you now only owe the remaining $200 when you file your taxes.
If it didn't account for the $20K payment and you forgot that you already paid, you'd be in danger of paying another $20K when you file your actual return.