My experience with BA/Flybe, when Flybe bought the BA domestic carrier was that for the first 6 months you got BA points, but from that point onwards it was nothing. Flybe does have a FFP on their own - not that it's much use for anything.
I can see that happening that the domestic flyers would be forced to use the Flybe program not to give out too much OW statuses. Just my 2 cents...