I believe they are right, it would be very hard to get the dent out completely. They would then finish it with a filler to get the right shape.
At least with a new trunk its not a repaired piece. Dont know about honda fort, but gateway have bake paint so the results are fine. Plus they would get the original trunk from factory, not from the open market. Insurance will pay them so they have no reason to cheat in this manner.
For your piece of mind, take pictures of the fittings etc of the trunk, and compare it afterwards so you are sure they did it properly.