Perhaps not, but it would seem like rank incompetence to issue one in the knowledge there wouldn't be a legal basis to take the matter any further.
Unless it's just a fishing expedition (this person has done a thing we don't like, which might have led to non-collection of an excess fare had we not realised they'd started short, therefore let's see if they've done anything else).
For what it's worth I think the guidance to ignore this sort of thing if no money has been saved is very wise and ought to be followed. The point of advances is to allow flexible pricing reflecting demand for specific trains. The OP is sticking to the booked train. He should get the less expensive fare. Even if he drives a little way down the line and gets on there. Not because he's entitled under the NRCoT or any other contractual term, but because it's a reasonable way for a business to treat its customers and the TIR route isn't.
A prosecution would be brought under the more serious Regulation of Railways Act 1889 because if it has got to that stage, it would be because the TOC suspected the customer was intentionally seeking to avoid paying the correct fare.
The guidance should definitely be followed, but this forum lives in a strange world at times where absolutely everyone is genuine and doesn't recognise that people trawl this forum looking for ways to avoid payment/defraud the railway, just as much as people trawl the forum looking for genuine assistance.
It's also very much NOT the case of "this person has done a thing we don't like" - the reality is "this person has contravened the terms of their ticket, that they agreed to abide by in return for a (usually) cheaper, yield managed Advance fare, and travelled without a valid ticket" - albeit 99% of the time, we won't enforce the breach, because it is sensible and good customer service and also bad publicity.
This is becoming a problem on certain Northern routes, where Advance fares deliberately aren't made available from intermediate points, but are available from say Leeds, where competition exists. People are intentionally "starting short" to circumvent the fare that is legally due.