If the circumstances were as the OP describes and the train manager's report was silent in the issue of permission, that would be a serious and misleading omission on the train manager's part.
Indeed it would be. But without having access to the report, we cannot know. And it would seem bizarre for the TM to be happy for the OP to board and yet seek to issue them with a TIR.
I wonder whether there was perhaps a misunderstanding - with the TM meaning "don't miss the train, get onboard", whilst the OP took this as "you have permission to travel without a valid ticket"?
But in this case there are there are 3 potential witness
1) The ticket person at Leeds (who couldn’t print them either)
2) The Train manager
3) The Trainline call handler that released them (once they opened for the day)
But both the first and last people would only be able to confirm that the OP had difficulties collecting their ticket (for "self imposed" reasons, i.e. nothing which could negate a Byelaw 18 charge), something which I don't think is in dispute.
However, the OP would have had an opportunity to buy a ticket at the ticket office, even if that would have been financially painful, and so I cannot see that any defence arises under Byelaw 18(3)(i) or (ii).
Of those three, it is only the TM who would be able to testify as to what permission they did or did not give.
Then there is almost certainly an electronic record of the tickets being released and printed in Glasgow. And of course a record of the Op buying the tickets before the journey (even if hadn’t been collected from machine)
Indeed, and this all militates against any intent to avoid payment existing. But a RoRA offence isn't really in question, since the OP had paid for their ticket prior to travel. Instead, the Byelaw 18(1) offence is not concerned with whether someone had paid for their fare, but rather whether they have a ticket on them when boarding.
Even the most ambitious TIL prosecutor wouldn’t expect success having to prove beyond doubt against that much evidence, they are used to people not having bought a ticket, or bought a cheaper ticket that is not valid
As the basic elements of the offence are made out, it would be for the OP to successfully raise a defence under Byelaw 18(3)(iii). I have heard of much less 'ambitious' TIL prosecutions in the past!
I am thinking it might be worth sending a version as a copy direct to customer services at Cross Country, if they appointed TIL, they can just as easily cancel the claim citing new evidence, or admin error, and it might be easier if they ask to discontinue the action.
There is certainly no harm in doing so - I don't think it will cause TIL to withdraw their offer of settlement and proceed straight to prosecution. And there is a chance, albeit small (in my view), that this could cause the matter to be dropped.