Some years ago microlights were not aeroplanes, they did not need a licence and operated for some time this way. Unfortunately there were a number of fatal accidents and as the devices involved were not legally aeroplanes the Ministry of Transport required some level of regulation. The BMAA dida good job of this and the D rating was born requiring a minimum of legal change; with it came the second tier medical or declaration for which there was absolutely no provision in the ANO.
When AOPA who dragged the PPL into the JAR realised they were not in control of the final outcome, started to attack the CAA re the JAA licence and were told to go away and not come back unless they had something constructive to say. They came back with the NPPL which was a reasonable proposal that could have been implemented with minimal law changes and the existing medical declaration arrangements.
Unfortunately a recently retired RAF Office seeking to make his name in the CAA, grabbed this as the ideal opportunity. All the initial work was done by people with no experience or knowledge of licensing, resulting in a tranche of unnecessary and bungled legislation. Realising that after the first burst of old group A licence holders who couldn't pass a medical had past, there would only be a limited ab-initio flow, the SLMG and Microlights were dragged in to make the statistics look better. Then followed the biggest dose of nonsensical beaurocracy and bungling ever seen ion the history of aviation.
All that was needed was the standard ICAO requirement (Because nobody does it in less) a second tier medical which already existed and a limitation at the UK FIR boundary.
Is there any difference in safety between a NPPL and JAA PPL
No, the standard is exactly the same. Nobody has ever brief examiners to do anything different, or should I say examiners have never even been brief with regard to the NPPL!