Neither - those clauses state the rules on which the response should be given i.e. that it has to be responded to, if rejected clear reasons why it is rejected and that the communication has to be separate from other communications. The clause that should be referenced in the response for rejection of a programme is clause 31.3, for which there are four reasons they can reject.
It is worth pointing out that NEC4 now says if the Project Manager is rejecting a submission, they should state the reasons why IN SUFFICIENT DETAIL TO ALLOW THE CONTRACTOR TO CORRECT THE SUBMISSION (the capitalised bit being the new additional words). This makes it clear they have to give specific reasons why rejecting to allow them to correct it, not giving high level reasons e.g. your programme is not realistic.