It wasn't very difficult or expensive to set-up company specific FTE training to satisfy EASA. I did it last year for a company doing a CS-23 aeroplane and I am now involved in a company where we must define and agree with EASA our own requirements because there are no rules for our type of aircraft.
In the UK, there is now the option for sub-2000 kg aircraft (not just aeroplanes) to use E Conditions and avoid EASA all together.
With this experience, I don't see the work to comply for pilots and flight test engineers as any more difficult or expensive than anything else to get a Design Organisation Approval. EASA may have made some terrible mistakes in writing rules but in my twelve years working with them they can be flexible and practical in making things happen.