Thanks @OldCrone I think you are right, it's definitely not for commercial reasons but for dissemination, which is similar to news reporting.
So I asked about numbers of people who complained
According to NR, they received 158 complaints as of 19 August. None of their complaints were through the official customer relations department and includes Twitter contact where Network Rail provided a response. It does not include all the Twitter converstions. I, obviously, did not make my request clear enough or maybe they are being obtuse - I wanted to know how many complaints they received before the poster was taken down. I will contact to ask them to clarify that question.
I also asked what the decision making process was to take the poster down
This was very interesting because there was a chain of emails, with the names and positions withheld. All emails sent on 28th July.
The first email is from the Times reporter who quotes Kelly-Jay talking about the ad in a video and wants to ask Scotrail if they have any comments and any complaints about the ad.
The second email is an internal one from a NR employee to 3 others talking about the Times Request. It has the subject line of JK Rowling / trans rights advertisement Waverley. They "dont think we want to be in this be in this debate". They are going to go back to the reporter and say there's been no public complaints and that they should contact JCDecaus about it. They ask the question if it need to ask JCD to kill it because it might breach their neutrality.
The third email says NR have a strict policy and "I guess this did't breach the policy? But dodgy ground nonetheless." It "might not strictly break the rules" and "could be seen as innocent support" but that "knowing the background its not wise." The email goes on to say that "its not our debate" and then it's a little bit about how this got through and what can be done about future ads.
The fourth email says "we don't want to look to be supporting anything either way". They've cc'ed someone who can advise whether it breaches their policy.
The final email (sounds like someone in charge!) says that they've just been made aware of the poster and to take . poster down. They've been made aware of the poster This email says because of the media debate surrounding JKR and her position on gender politics it breaches article 5 of the Code of Acceptance and it needs to be taken down.
I asked them about the Code of Acceptance policy for ads
Article 5 says: "It is of a political nature calling for the support of a particular viewpoint, policy or action or attacking a member or policies of any legislative, central or local government authority.
There you have it.