Unfortunately, as per
Regulation 9 of The Railways (Penalty Fares) Regulations 2018 it is indeed correct to issue a Penalty Fare on the basis of the "full single fare" (note this is a different kind of "full single fare" to the kind the NRCoT talks about) from the boarding station, even if a valid ticket was held for part of the journey.
However, there may well be other grounds of appeal, particularly including signage. Having previously used the Stansted Express on a number of occasions, the Penalty Fare signage when entering the gateline/platform is woeful in size and prominence, and I am almost sure it will not include the required wordings.
If your friend wishes to take the matter further, he would be well advised to pay the Penalty Fare, and to then submit an appeal against the Penalty Fare on the basis of any deficiencies he finds when comparing the signage present at Liverpool Street to the requirements set out in Paragraph 1 of Part 1 of
Schedule 1 of the Regulations.
If he wishes, he could (or anyone else who happens to be passing through Liverpool Street station who is reading this) take pictures of any signage that is present, and upload it to here. We will then be able to analyse the compliance (or otherwise) compared to the requirements of the Regulations.