penalties for late payment

Hi Tax Tutor, please, I am not clear about the statement that “penalties for late payment do not apply to late payment on account” and penalties for late payment apply to:
1.balancing payments of income tax and class 4 NICs and any CGT under self assessment or a determination.
2.Tax due on the amendment of a self assessment.
3.Tax due on a discovery assessment.

does that mean there is a difference between payment on account and payment under self assessment. please clarify further.
thanks in advance