EM6101 - Contract Settlements: Surcharge: Outline
The guidance about contract settlements at EM6000+ only relates to direct tax. You must never include VAT or VAT penalties in a contract settlement.
For ITSA years, surcharges are payable on any tax and Class 4 NIC which remain unpaid more than 28 days and more than 6 months after the due date. See EM4100+.