Una due TFC;
You raise a valid point. Aer Lingus could certainly do a deal with any carrier to operate as Aer Lingus Regional. But it's unlikely as
1. A contract is in place until 2022 ( dates from memory )
2. EI have a vested interest in the fleet of Stobart Air, funding some of the ATR's but I don't know if that is still the case since Stobart Air came about
The model works well. My guess would be EI could certainly go in house and set up its own commuter carrier if it parted ways with Stobart Air, but again very hypothetical.
Regarding 'protection', I can't see how they would have any protection on any route , we operate in a deregulated market. They don't get much protection from Ryanair's predatory behaviour of widely available €8 one way on DUB BHX and MAN. Gladly, EIR have the point of difference of interlining traffic !