I don't understand your second paragraph at all.
Using a Manchester to Bolton ticket on a Manchester to Bolton train, what offence do you propose is committed? How is this different to using a Bolton to Manchester ticket on a Bolton to Manchester train!?
It was very very profitable for FGW: they had a long train full of people they could charge the anytime day single for the journey (>£100, +administrative fees if they don't pay), and then charge them again for a ticket home.
I'm confident it's not about saving seats for those going further...