Jambo,
I have to agree with a defence of any Training/Flight Ops departments. These are generally (although not always) run by pilots for pilots. There intentions are to improve the knowledge, skill and safety of al pilots in a company. I don't doubt that this is the case, even in RYR.
My problem is with "Commercial Management" as you call it. I have seen many cases in various airlines of training or ops departments having their hands tied by the "upper echelons". The attitude of an airline comes from the top down.
With the licencing thing, although I agree that the home state should be responsible, at the end of the day, it is the RYR training departement (undoubtedly with upper echelon tied hands) that are ultimately allowing these people to fly, not the German/French/Dutch/Whereverland authorities. An authority gives you the licence. The airline gives you the aircraft to fly.