Something to keep in mind: The prices are not souly based on their cargo hold. They are based on where they can operate, how many/what type of guns they have, how much armor they have, etc.
So with these factors involved it may give a better insight as to why some prices are different.
Or in simpler wording: Civilian transports cost more than their house tech counterparts.
Even though all those factors mentioned above count in the price of a ship, the main InRp reason for the price difference is that houses have access to larger facilities and cheaper materials than the civilian market, which is why the house-built transports come in cheaper than the civilian ones. Compare the price range of ~3k transports and you'll clearly see this difference.