All the prosecution has to do is go to the Court and say that in respect of the case against "X" we are no longer continuing with the prosecution.
As I said, the words "the case against John Smith" seem to me to mean - regardless of whether they are used to the clerk or the magistrates - that there is a real defendant in this case called John Smith when there isn't.
The company cannot control what the clerk says to the magistrates and so cannot control whether the clerk misleads them.
But even if a form of words is used which does not imply there is a real defendant, there is still some difference between situations where:
a) the company is offering a settlement for having its *own employees* misled (ie avoiding conviction under the Regulation of Railways Act),
and
b) the company may get more money from the passenger after the *court* is given the false name and the passenger wants to avoid a conviction under a different law.
The first one involves a settlement for an offence that in a meaningful sense is more concerned with private loss to the company.
The second is more concerned with the passenger's effect on the legal process, and is in a meaningful sense more of a public matter. So we might ask whether it is appropriate for a company to be holding that over the passenger when proposing a level of financial settlement.
If a case is withdrawn there is no verdict!
As I said, I was referring to the other suggestion - that the company could knowingly let the case with the false identity go to a verdict. It is nothing to do with the case being withdrawn.