I do not believe attaching anything to the tax return is really read. If it makes everybody feel better, fine. Reality is that you need to wait for the notice (and tell the client they will get one.) "undue confusion for the IRS" - They already got that, so I think you would just add to it. 

They will definitely owe the interest on the money, but I think a good sob story will get them out of the penalties. 

P.S. I would just wait for e-file to open and efile the return. The client could go ahead and make a payment for the return NOW at https://www.irs.gov/payments/direct-pay