I broadly agree with this.I work as a contract manager and am always mindful that if a dispute were to arise, it is the written agreement that will tend to prevail, and any "evolution" would need to be proven - usually quite onerous, and liable to bring out quite a lot on the way.
I'd also observe that the case is based on the impact of the alleged anti-competitive behaviour on farepaying passengers, and therefore that whether "the industry" did or did not approve of GTR's conduct might in fact point to guilt (as evidencing cartel like behaviour) rather than innocence.
As the TSA is a contract between RSP and the operators, I'm not quite sure (but IANAL) how it is that the actions of GTR in selling brand level tickets not provided for in the TSA could be actionable by a customer who is not party to that contract. However, the arguments about anti-competitive (and anti-consumer) behaviour seem at face value much more compelling.
Though I'll point out that a customer in dispute with the TSA does not need to refer to the TSA in any dispute with the company.
To the best of my knowledge, all complaints and requests for refunds of excess fares, penalty fares, additional fares charged to the holder of a ticket that was rejected for use on the 'wrong' brand, that I've been aware of, have all been refunded. I've certainly not heard of any cases where a refund was not forthcoming. I don't recall any cases being escalated to the Rail Ombudsman (or Transport Focus, pre-2018).