There's tons of circunstancial evidence that the RAF converted the Spitfires and Hurricanes. Loads of it.
A couple of things to also think about..
1. The modification to the boost cut out control that was needed was (AFAIK) one way, once done it meant you couldn't put 87 octane into a converted Merlin
(This is my understanding of it, correct me if you know better
)
2. At the time of the changeover the RAF painted '100' next to the fuel filler cap to ensure that the correct fuel was put in. I have literally hundreds of photographs of BoB Spitfires and I have yet to find a photograph taken during the BoB that shows a Spitfire or Hurricane with this feature, which suggests to me that the need to differentiate between the 2 types of fuel was no longer there, ie. all converted.
Also several RAF pilots state in their memoirs that the conversion took place 'just before' the BoB proper, Tim Viggors, Pete Brothers, Al Deere are recent ones I've read.