The Pipe Bolt-action gun has its base damage raised significantly to account for the fact that it uses the rare and expensive. The Pipe gun has it's base damage raised to equal the 'Deliverer' gun that you get for completing the first railroad quest.
If you're like me, you enjoy the immersion of playing with these weapons that you looted from some raiders but don't want to sacrifice the damage loss compared to all the other weapons that are available. Craftable versions of the Pipe Gun and the Pipe Bolt-Action Gun with higher base damage.