That's the problem. Fixed penalty is only available for salaried class. For self-employed / business persons, penalty is based on percentage of tax. For salaried class, its all automatic. While for self-employed, application will be approved by commissioner, or after 4 days it will be automatically approved if the commissioner doesn't approve/decline it.
From what I see, penalty is only available for salaried class. For self-employed, you take amnesty if you did not pay full tax in first place as it says "revision of return" not penalty. If you paid full tax or you are tax exempt, you have no option but to get audited. That's my understanding.
I think its better to contact FBR. I emailed them in last amnesty and they did reply in 3 days.