Can one apply for SONCAP certificate after the consignment has left the country of origin? What is the penalty of not conforming to the SONCAP scheme prior to my consignment arriving in the country?

No.

The SONCAP is an offshore and pre-shipment certification scheme, thus, cannot be processed after the consignment has left the country of origin. What is applicable at this stage is the SONCAP Default, which shall be charged at 20% CIF of the consignment or 2 million Naira, whichever is higher