That would be an incredibly niche activity (even given where it would be possible, i.e. only on nights when the Night Tube runs and only on those routes) and thus really isn't of any sort of concern whatsoever.
Would be popular with the tissue beggars!
But for practical purposes where can that fare be? In the case of Manchester - Chester it will probably be a flexible single for about £13, with some similar prices for Advance tickets to today but in much more restrictive quota. If you made it about £5, which would be where I'd put it then you'd never deliver the capacity.
£13 is cheaper than the cheapest walk-up single sold at the moment (the Avanti one, which people frequently get tripped up by because there's a limited number of valid itineraries).
So any simplification means much less efficient revenue management: your choice is busy trains being so busy that people are standing in the aisles and at risk of being left behind, or trains during most of the day with vacant unsold seats.
The revenue management on this route seems to be rather cack-handed with far too generous quotas on the busiest trains. It feels like cheap Advances are being thrown about like confetti for the busiest trains. People already get left behind on some days. At the moment you either get a bargain or you get ripped-off. The £13 you mention above sounds a reasonable (generous even) compromise for the journey in question.
So while it's easy for train conductors to whinge that it's all the pricing manager's fault - it's actually down to their revenue management expertise that the industry has grown as much as it has in recent years
So when someone has already paid for their ticket but I am charging for a new one because it is for the wrong time or wrong operator, is this helping to grow the railway as a whole or are these TOC-specific fares between Chester and Manchester just affecting how big a slice of the pie each operator gets while destroying passenger goodwill?
Anyone who thinks it's sensible for the London - Birmingham stopping trains to cost the same as Avanti on the day of travel is kidding themselves.
From what has been said on here about loadings on the Birminghams, Avanti is overcharging and prices could be cut without risking a capacity crunch. Obviously once HS2 opens to Euston capacity is expanded yet further. Likewise I suspect that the ridiculous Anytime fares between London and Manchester could come down without causing a capacity crunch - they've distorted the market such that the Off Peak trains are much busier.
I can however see a justification for the differentiation on the Trent Valley, where Avanti trains are generally full and there is a need to price people off of the intercity services and use the stoppers as a budget option.