If they want to be in compliance with the NFIP, they better be requiring that each structure is adequately covered by a separate policy either through the NFIP or a WYO.
The only possible exception, and this is pure speculation, is if the flood policy is being written through a private insurer. In this case the policy is not written through the NFIP and one policy may be sufficient to cover all buildings. However to repeat, this is speculation and I did not research it, nor have I dealt with private insurers.
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The opinions expressed are mine and they are not to be taken as legal advice.