Can you confirm if this actually worked when they processed your amended return?
Amended returns are manually reviewed and processed. Penalties, including underpayment penalty, are not explicitly waived or removed through an amended return. I think IRS has a different process for dealing with penalties called, "abatement"
What the advice here has basically told you to do is treat the penalty you paid as an additional tax deducted from your refund. I'm not sure that's going to pass muster with IRS, however.
