Simple - resources! both that of the FTO and the airline.
Flybe take many recruits from many places and it would be impossible to take all MPL. There needs to be a large gene pool in any airline with the mix of experience, expertise and talent. It may be that in the future MPL is the way to go but it is really in its infancy right now.
The MPL candidates will not be in competiton with the integrated or modular students. Like the MAPS schemes they will have a job before they start training - nice feeling!