Questions on VAT penalties and foreign business

I have two questions I would like you to assist me to resolve.

1. When a business fails to register for VAT tax upon reaching the registration threshold, out of ignorance, until it comes to light months later how does one avoid maximum penalty and surcharges?
This came to light at the time of preparing the annual accounts for the trader. Trade is hair salon and attached food shop.

2. When one who is a UK resident and ordinary resident trades, I know that tax is assessable on world-wide income. However, for a non domicile I understand that income is assessable to UK tax only when it is remitted to the UK. Is my understanding correct?
Also what do you do to the business expenditure like port and handling duties paid in the foreign country where the goods are sold? In particular where these expenditure far exceeds the reported income from the foreign country? Would the Revenue allow all these foreign expenditures, albeit business related expenditure?

Gabriel Bonsu