The court process has become confused because you requested a hearing to make an application for the magistrates to re-open the case in the interests of justice. They have scheduled a hearing for that application. Theoretically, if you served a statutory declaration on them within an appropriate timescale that should, I think, take precedence, but it may be that their systems and processes couldn’t cope with that. This leaves the nature of the hearing somewhat opaque, but they will want a plea as soon as possible so they know whether to schedule a trial or not.
It is always open to a criminal defendant to plead not guilty and to require the prosecution to present its evidence. There is a larger sentence discount if a guilty plea is entered at the first opportunity but there should still be some discount if a defendant changes their plea at a later point, such as before the start of the trial. If you plead guilty then the train company can do nothing, and the court process will continue. Pleading not guilty should, I think, mean they’ll then be notified of a subsequent date for a trial. I don’t think you’ve seen a copy of any witness statement or more detail than the charge information sent by email, and its logical not to plead guilty to something where the exact details haven’t been made clear.
You may want to be prepared to discuss the procedure with the court and its legal advisor - I think your position is that you made and served a statutory declaration but it’s possible the court won’t be aware of that depending on how their systems are set up. Taking proof of that, and proof of service, could be helpful.
