We played our first game with a transport last night. Great fun and a victory for the Imperials. One question arose but was not an issue as the player did not use 'Backstabber' in the end.

The issue is does 'Backstabber' get to use his ability when attacking the transport at all times as it does not have a fire arc?

No, the FAQ clarifies that a ship has to have a firing arc for backstabber to be out of in order for his ability to work. That precludes the senator's shuttle token from the core set and now the transport as well.

The relevant question in the FAQ is on the last page, in the section on missions (for some reason), and says

Q: Is Backstabber outside the firing arc of a ship that has no printed firing arc?

A: No, Backstabber’s pilot ability only triggers against ships that have a printed firing arc.

Cheers must have missed that.

Just a note. You may have missed my edit saying exactly where the relevant FAQ entry is.

Using that part of the FAQ may be an effective stopgap, but I'm leery of making it the absolute final say on the matter. There are a couple parts of the FAQ that give different rulings for different aspects of the game, and since that ruling falls under the missions category, I'm not entirely convinced it should be used for Epic play.