What we have at the moment, de facto at any rate, is the railway saying that for an advance both a split ticket and a through ticket mean, for example:
"Assuming you get to Scarborough station in time, we will carry you on the 11:34 from Scarborough to York and the 12:32 from York to Kings Cross, and if you catch the first train but miss the second, we will carry you on a later train to Kings Cross, and pay you compensation if you arrive in Kings Cross 15 minutes late or more."
What they could decide to say, for those purchasing tickets after the new NRCoT come in, is that a through ticket from Scarborough to London Terminals retains the above meaning, and a split at York with separate advances will then mean:
"Assuming you get to Scarborough station in time, we will carry you on the 11:34 from Scarborough to York. If you get to York on time, we will carry you on the 12:32 from York to Kings Cross. If you don't, you will need to obtain a new ticket to continue your journey. We will pay you compensation based on the price of the ticket you were using at the time you incurred the delay if the train arrives at the destination printed on the ticket more than 15 minutes late."
Nothing stops the railway from changing the terms upon which it will offer tickets, and nothing forces customers to buy them on those terms or any terms at all. A customer wishing to be protected in the event of a missed connection retains the option to purchase a through ticket. To the extent this is at a higher cost, it is no different to goods and services purchased elsewhere, where one generally tends to pay a higher price for better quality.
In the (currently theoretical) scenario I've just described, a customer would retain the right to claim damages, including consequential losses such as the cost of a new LNER ticket, from TransPennine, though such a claim would likely require the passenger to prove that TransPennine were at fault for the delay.
In short, all these changes, which the railway is at liberty to make, would serve the purpose of discouraging the use of split ticketing, which is undoubtedly irksome and customer-unfriendly, but does not appear to me to be illegal.