Flybe's definition of "one stop modular" is simple. They want candidates who have done the CPL and IR at the same school. That's it. It does not include MCC, ATPL writtens or PPL.
The reason, and this is from a definitive source, is so they can check a candidate's training records quickly and easily, rather than having to speak to half a dozen schools and get the story bit by bit. In other words, it's an audit trail.
Any employer wants to minimise their training risks, and Flybe have obviously decided that continuity of training is a significant factor. 'Fairness' doesn't come into it - it's their trainset and they decide what selection criteria to use.