The two documents are not interchangeable. Here's the difference, and what to ask for at each stage.
A Certificate of Occupancy proves the state has granted you a 99-year right of occupancy on a specific parcel. A Governor's Consent, on the other hand, is the state's approval of a later transfer of that parcel from one party to another.
If a seller hands you a C of O in someone else's name and tells you 'consent is in process', what you actually own — until consent is perfected — is a contract, not the land.
Before signing anything, request a charting report from the Lagos State Lands Bureau. It costs a fraction of the deposit and tells you whether the plot is under government acquisition, committed or free.
