My guess is that someone in the DfT or LNER has expressed an opinion that revenue maximisation on LNER would be aided by ending the acceptance of regional rovers on LNER services. And by a process of Chinese whispers we get the story told by the OP. Given that we are currently in a period of many fares being frozen by government edict the optics of such a change to rovers would be terrible.
Yeah, on a London to Halifax trip a couple of years ago it proved cheaper to use a Hull Trains Advance Single to Doncaster, an Anytime single to South Elmsall and a West Yorks Day Ranger proved a considerably cheaper option than anything involving the Advance Singles LNER were offering to Halifax or Leeds.
I was pleasantly surprised how readily my South Elmsall and Day Ranger combination was accepted for the non-stop split on an LNER service, but wouldn't be at all surprised if management at LNER dislike the validity of such combinations and would prefer it if anyone too tight to pay their Advance fares was priced off onto other operators for the entire journey, or just priced off the railway entirely.
I doubt there's any significant revenue loss or impact on capacity given the vanishingly small number of passengers who buy Rovers at all, let alone use them as part of a longer journey in this way.