By the use of SQEP (Suitably Qualified and Experienced Personnel) staff, who have the appropriate skill and qualfications to review, monitor and audit. It isn't rocket science, but needs both sides to be professional, diligent, aware and not cut corners. At times therefore it may be initially painful, but ultimately beneficial.
I'd question how independant the CAA is of Government as it is funded by them and sits below DfT. Probably not too much more or less than the MAA in many ways and effectiveness. The real difference is between the MAAIB and AAIB and the MAA and CAA!!