I've already explained why I disapproved of it, by way of positively explaining what I believed were misconceptions about The Manual entry and where such complaints could be more effectively targeted.
It is the case that many railway staff have no idea what significance, if any, the National Rail Conditions of Carriage bear to railway travel. It is therefore immaterial whether the conditions are presented to staff on A4 paper or a fancy blue booklet. Even in my four week retail training, only fleeting references were made to the NRCoC, the rest was custom made material which was derived from its contents but neglected to reference the NRCoC most of the time.
You said "It does not say that staff are not to print out a copy of the NRCoC on request, if possible". You are entirely correct that The Manual entry doesn't prevent that. The problem is the "if possible". There is no "if possible" about it. What The Manual does say is "the NRCoC no longer has to be published in paper form and so it is now available only as a .pdf document ... enquiring passengers should be referred to the National Rail Enquiries website" which is clearly instructing ticketing staff that they are not required to provide the NRCoC. Unless ticket offices are routinely displaying the full NRCoC for public consumption then this is simply wrong (see my post of yesterday).
Therefore, while you could claim there was a "misconception about The Manual entry" if ticket offices were publicly displaying the NRCoC, I think we can all agree that ticket offices are not doing that. By not making it abundantly clear that there is a positive duty (i.e. a duty without any "if possibles") to provide or give access to the NRCoC, The Manual is simply wrong, and is causing a significant problem. In this particular case it is very clear that the ticket office had positively refused to make the NRCoC available, and I do not think it much of a jump to suggest that The Manual entry is responsible for this; it certainly doesn't help the situation.
This is a serious problem for both passengers and the railways. For passengers, because they potentially cannot access the t&c's they travel under (note that I am as eager to see passengers held to their responsibilities as I am to see them given their rights); for the railways, because there's a risk that any attempted enforcement or prosecution is open to a challenge that they have not met the requirements laid out in Thomson v LMS and elsewhere (IANAL, obviously). More broadly, if as you say staff are more likely to use The Manual and related material than refer to the NRCoC direct, what else are ATOC getting wrong?
Now, was bringing this to the attention of the DfT appropriate, as opposed to a quiet word in ATOC's shell-like? Frankly, I think it was. ATOC are a well-funded organisation, they are capable of reading the NRCoC and providing instructions that allow their members to stick to it, and they have manifestly failed to do so. A complaint to the bottom rung of ATOC is unlikely to give speedy results, not least because as an organisation they work in their members interests, not the passengers. Whereas the DfT are responsible for balancing passengers with TOCs, and have a duty to reply with the relevant information. There are situations where a problem is so egregious that it's legitimate to jump a few rungs to get to a point where it can be fixed, and this is one of them.