There are certainly two sides to this last argument, depending on the 'flight safety criticality' of the mods.
With the sheer amount of clearance work going through Boscombe, waiting for full MARs is not always necessary, and there have been a number of examples of aircraft operating with great success under OECs (Operational Emergency Clearances) and Sevice Deviations. This is, however, perhaps only possible with modifications to old and familiar types in which there has already been considerable iteration between the design/development, testing and frontline world's. Streamlined procedures which may have been appropriate for rushing the Jaguar UOR or J96 into service may not be appropriate for a DA Mod which is presented (sight hitherto unseen) to the RAF by the OEM. But to insist on crossing every T and dotting every i every time would just cause even greater delays and cost.