Hanoi to Hong Kong

There´s no border control at Nanning Railway Station, it's at Pingxiang, where you can apply for the VOA.

So how do I get the transit visa? or do I just keep travelling by train?

There's no need for a transit visa but you have to apply for a visa on arrival as you transit in 2 chinese cities.
You'll get it at the Pingxiang border control.
But I have no idea if it works as it's a small border control and they may refuse you.
I would contact them in advance as Pingxiang is the only office which can give you a 100% answer.

You will need to apply for a visa in advance. Its not a valid entry point for the transit without visa.