That is a fair point and the best argument I have seen on this subject. But I would argue that the list expressly included I the contract (or expressly referred to on the National Rail website) still supersedes the first part of the definition.I don't see it as being unambiguous - there are two parts to the statement.
There is a list of current licenses in operation here
Govia Thameslink Railway Limited
Southern Railway Limited
Gatwick Express is not listed separately. I'm not so sure about Southern being separate as they have transferred all their liabilities to Govia Thameslink Railway Limited.
Just because they then go on to say a list of companies can be found in the appendix, doesn't change the fact that the companies in the appendix don't meet the definition that they have included.
I'd say that's a very real case of ambiguity - and generally when there is ambiguity in a contract it should be interpreted in favour of the person who didn't draft it.