That's not the whole story, Cathar.
Firstly, the CAA describes itself as the aviation consultant to the UK Govt. So it's no use anybody pretending that the CAA is some independent body and the DfT is another. They all know each other by first names; this is evident when one phones up one bit or the other. They could just as easily all be in the same building and be the same Govt department.
Secondly, JAR-FCL is not binding on JAA members. For example, the UK automatically validates ICAO licenses for VFR privileges in a G-reg, and allows an ICAO IR for IFR OCAS. Another country could equally validate ICAO IRs for IFR in CAS.
EASA will soon be taking over FCL, but does that mean an end to ANO Article 26 and the automatic ICAO license validation which the UK does? It would also mean a total end to ICAO license validation (automatic or not) throughout the EU. I don't think EASA is going to force that because it would deprive so many EU-resident pilots of their flying privileges. Such pilots would be forced to move to own-reg planes and then EASA has to deal with the much bigger (and much more controversial) fish of foreign reg planes based here.
Certification, I agree, is something else and EASA is already getting its teeth into that. I doubt any JAA state is going to accept FAA certification; well not without formality. The CAA used to issue AANs for FAA STCs, under a bilateral treaty with the FAA, until they signed up to JAA, and possibly for some time after that.
But as I say EASA has much bigger fish to fry; for example they can't simply screw Airbus sales in the USA by doing some "on principle" action against N-reg planes based in the EU. They are much more likely to use a carrot than a stick.