I asked about this two or three times before release because of these kinds of statements, and I never got an answer.
There is nothing that says a Junker cannot land his pirate train (the largest ship he is allowed by his ID) on lawful bases (except lawful kusari bases).
I would be pretty annoyed if this got changed, since I asked about this a couple of times before buying my pirate train, and now own a pirate train on my junker, with largely unlawful, but some other places involved (IMG and zoner bases, that sort of thing. Maybe even lawful planets for semi-dirty goods (stuff like small arms, tobacco, blood diamonds in the houses they're not illegal)
I possess the exact same problem. I have a Junker character named Kubotan, piloting a Pirate Train.
Now, I was not notified anywhere up until this point that characters piloting a Pirate Train are not allowed to dock on lawful bases. There should exist an exception for Junkers since the whole point of being a Junker is to act as the "Middleman" between lawful and unlawful parties. Now if the ID to the respective faction also states that you can pilot a vessel which maximum carries 4300 cargo, I assume the ID is trying to indicate that the Pirate Train is your best financial choice of vessel if you are a Junker, and it certainly is not if you are not allowed to be just that, the Middleman.