Ryanair will ensure one way or another that their pilots (whether they be contracted or BRK) will be registered with the IAA. Financial penalties are to be applied to both sets if they refuse to abide. I suppose it depends in how much you value your licence with your issuing authority in the end? I also see that any CUs or training positions are stalled if the IAA licence isn't in possession.
I agree that with over 2000 pilots with over 25 nationalities, licensing could become a real headache. The Turkish airline with the Swedish crew member flying around for 13 years without any valid qualification indeed highlights this.
Yet I also agree it is a bit hard to take, especially if you hold a blue or green CAA issued book which any IAA TRE can endorse. However there won't be a rule for one and another for the rest! It's either IAA or salary deduction it appears.
Still, have to wonder. The IAA make a nice little earner out of...well..doing very little. I wonder what Ryanair achieve from the IAA in return??