The TOC-only pricing from Wilmslow to Manchester has changed over time, as I think has happened in a lot of places on the WCML. Initially the Virgin Trains price offered a significant saving over the Northern-priced any permitted fare with a reduction in flexibility. It was a useful option and I used it frequently.
Now the TOC-only fare is 10p less than the "any permitted" fare, so it's pointless (for 10p more I get 3 more trains per hour, and the option of the route via Manchester Airport, and the opportunity to break my journey at places other than Stockport), and only exists because it will show up first on booking Web sites, and be chosen by people who don't know any better.
It's a game being played at the expense of the paying passenger, who is completely confused by railway pricing anyway.
I don't think they should be abolished, but I think it just means that people are frightened away from using trains because of the complexity and should approach ticket purchasing with appropriate cynicism and caution. If we accept that TOCs want as much of our money as they can get, then these are the games they will play, along with other companies which "reward" customers by charging more at renewal than they would for new customers.
I have spent a lot of time and effort over my life understanding railway ticket pricing, for me it's a game and I play it to win, however the vast majority of people who buy rail tickets don't have my knowledge and interest.
If we're going down the path of effectively nationalising our railways as we seem to be, there are a number of predatory practices which shouldn't happen, but TOC-only fares are not the problem, it's the way that they're now being implemented that is the problem.