In analysing Flybe's modular preference for no more than 2 FTOs for training, forget anything and everything to do with PPL stage training.
They are talking about commercial training only, and yes, I believe this also includes the groundschool.
However, remember, Flybe are only one of a large number of airlines/operators where you can start your commercial career. Go down whichever route best suits your circumstances, and which you believe gives you the best chance of gaining that licence. Don't blinker yourselves to just one potential employer, however good a place it may be to get your career underway.
Once you have a certain level of genuine commercial experience under your belt, the world is your oyster and all this will seem trivial and irrelevant. A bit like your school exam results once you've been working for a living for X number of years.