The note you highlight is intended only to guide the document compiler at tender stage. It should be deleted prior to tender, along with all the ‘If...applies’ notes found in the generic contract data. Look at how the NEC4 Engineering and Construction Short Contract (ECSC) deals with this as it puts such notes in boxes and explains these are not part of the contract.
The note is just highlighting the importance of filling in the contract data correctly. For example, if you select option X6 in the opening part of the contract data, make sure you correctly complete the associated X6 entries correctly found a few pages later. The contract would be incomplete if you stated option X6 applies then did not add in the daily bonus at the appropriate part of the contract data. It is not necessary to change the wording, but perhaps this is not as clear as in the ECSC. It is perhaps best either to delete these guidance-type comments when going to tender or include them as non-contractual statements.