You must *NOT* unmark the IRA/SEP/SIMPLE box if it's marked on the Form 1099-R provided by the payer. Failing to mark the IRA/SEP/SIMPLE box when it should be marked can create all sorts of problems.
As macuser_22 indicated, it seems that the IRS is not following their own published instructions for when line 4a should be blank. The IRS has not made public the changes to the Internal Revenue Manual for 2018 with regard to retirement distributions, so it's possible that the IRS instructions for Form 1040 lines 4a and 4b do not agree with what the IRS currently has in the IRM.
