Indeed, it's only modeled after real life numbers in a loose way. Realistically a ship's purchase cost would be a lot more than a truck and cost much less per km per tonne (but much higher per km) to operate. In pak128 (and other paksets) the capital purchase cost is adjusted down. For example, a bus costs about 20,000 and a large ship costs 500,000 to purchase (in modern day dollars this is more like $200,000 and $50,000,000-a factor of 10). Operating cost, at a guess, is probably around $1-2/km for the bus and several hundred $ per km for the ship.
The quandary is this: if you provide the player with $150,000,000 to start their transport company so that they can buy a couple of $50,000,000 ships, they don't have much incentive to focus on road transportation except as necessary to feed their ship network. If, however, you smooth out the costs to be more comparable, then the player can make similar profits from all of the various forms.