Why can't I file a Schedule C for the business owner as if the S-Corp 1099'ed him and report both EE and ER portion or payroll taxes on schedule SE?  Technically I should force the Schedule C QBI deduction to zero but it just does not make sense that Rev Proc 2013-30 allows retrospective late election, and there is no corresponding payroll tax filing process in place to facilitate this.  

In nature the S-Corp did pay the 100% owner as a 1099 contractor, and I think the QBI deduction is appropriate too.