This is a good example of an initiative that is passenger-friendly in theory, but not in practice. The passenger-friendly element can't survive contact with the TOCs.
If a claim has been made to TOC A and forwarded by TOC A to TOC B, it should not be open to TOC B to reply to the claimant rejecting the claim on the basis that TOC B wasn't responsible for the delay. They should send the claim to the TOC they think was responsible (even if that's TOC A).
Otherwise, you get this problem where any claim for a journey involving more than one TOC can very easily get forwarded inappropriately and then rejected not because the claim isn't valid, but simply because it's been forwarded inappropriately.
Personally I would much rather, if the TOC I've claimed from thinks another TOC is responsible, that they replied to me to tell me that. That way I can take the matter up with them if I don't agree. If I really have claimed from the wrong company then it's not especially unreasonable to expect me to fill in another form.
(It may be, of course, that ministers are quite keen on any initiative that makes it easier for TOCs to reject delay repay claims, since they don't seem to think passengers are paying enough as it is so won't like giving money back, and (paradoxically) they do not appear to want people to travel by train and seem oblivious or indifferent to the impact driving down passenger numbers will inevitably have on revenue).