I am not sure who you deal with to obtain your mortgage. If it is any one of those mortgage brokers, I can almost assure you that they are lying. What you can do is to state in your contract that you will only close contingent on the seller's successfully obtaining of the C/O. If the seller does not agree, the deal is off.
Do you know that you can be forced to knock down any non-conforming structure, even if you purchase the house, yet still responsible for the entire mortgage amount?