The only reason that the IRS might legitimately treat a code J8 Form 1099-R with a zero in box 2a as entirely taxable is if they did not receive any explanation indicating the original contribution that was returned; without explanation mentioning the Roth contribution that was being returned the IRS might assume that the Roth IRA custodian incorrectly reported the distribution and that it constituted a regular distribution instead.
The explanation that you are reiterating to the IRS should be sufficient to convince them that the distribution is not taxable or subject to penalty, but IRS examiners sometimes still get it wrong. Sometimes the help of a Taxpayer Advocate is needed to convince the IRS of the IRS's error.
