Can I write to IRS request waive penalty for late payment for client?

You can always ask, but with the information you provided it would be very unlikely they would waive the penalties. 

Interest:  No.  Penalty:  FTA.  Or maybe George and Ironnie know more than I do about why first-time abatement doesn’t apply to your client.  

Bob already said FTA, but worth spelling out since it's probably the whole answer.

Extension was timely and the return went in during June, so there's no failure-to-file penalty here — just failure-to-pay at 0.5%/month plus interest. Usually smaller than the client fears.

FTA is an administrative waiver, not reasonable cause, so you don't need a story at all. Just: no penalties in the three prior years, all returns filed, and the balance paid or on an IA. That last part matters — FTP keeps running until it's paid, so get it paid or set up the IA first, then request. Otherwise you're abating a moving number.

And don't write. Call PPS — FTA usually gets granted right on the call, which handles IRonMaN's point about interest running while you wait on a letter.

Interest: no. 6404(e) only covers IRS error or delay. But interest on the penalty comes off when the penalty does.

One thing — don't lead with the direct-debit mix-up. Under Boyle that's not reasonable cause for a payment failure, so it only hurts you. FTA doesn't ask why.