I e-filed a return, then several hours later e-filed an amended federal return as I overpaid a few hundred in the original return due to an error with TurboTax pre-filling incorrect values. After e-filing the amendment, TurboTax asked me to print and mail the remaining amount owed (form 1040-V) although I had already provided my direct debit details in the original return for debiting the original amount owed in the next few days. So I assume TurboTax simply doesn't reflect in the amended return that the original amount owed is already accounted for via an upcoming direct debit, and I can ignore TurboTax's request to mail a cheque for overpayment. I'm sure the IRS will realize this.
In the future, TurboTax should update form 1040 to reflect the original amount owed was accounted for, to be accurate and avoid confusing the client. But fortunately TurboTax is unlikely to be my first choice next cycle due to additional issues like I mentioned at https://ttlc.intuit.com/community/taxes/discussion/re-warning-turbotax-pref[product key removed]rs/0...