All defects and omissions covered by the MWC/EIC should be rectified before isuing the cert.
Only defects in the existing installation should be noted in the space provided.
Any departures from the Regulations, should offer the same degree of safety as would be achieved by compliance, and should be listed in the space provided for departures.
You will be signing a document that states the work complies with the Regulations. If you decide that supplementary bonding is required, then you must provide it, for the work covered by the MWC at least.