there's no way out of the 6% penalty for 2015, 2016 or 2017. Is that correct?
Not necessarily. Have the taxpayer remove all excess contributions now. Write a letter with a sob story explaining how the excess contribution happened, that the taxpayer corrected it as soon as possible after finding out the error, and that the taxpayer now knows & understands the income limitations and will monitor the situation more closely to avoid this situation in the future. Include all 5329s with the letter and send it without payment. Request a waiver of the penalty.