RE: Concerns about cost:
I think the prices are reasonable.
I would point you to the RMFRP Treasure Companion, p10, "societies with banking will be wealthier than those without". Plus the rest of the first chapter talks about the type of market needed to justify magically fantastical items.
Sel-Kai is ran by Merchant families, there are multiple banks in the city. As long as the cost of maintaining the ship is less than the profit it brings in (over its expected life) it makes sense. The heightened cost of a skyship needs to justify not building 10 or more traditional ships. And its time to market and range of market that does this.
The value of an aircraft:
The advantage of flying "straight" across a continent and back at speeds of 30-50 mph (barring breaks for Essence Storms and airborn monsters) means goods from greater distances can be brought together without resale to merchants in-between. Sel-Kai is profiting and growing by circumventing the traditional distribution and resale markets.
It works even better once the merchants moved the exchange to Sel-Kai, so if you are near the northeast of Emer, you send your wares to Sel-Kai sell them to one of the merchant families for a profit, and they distribute your goods to a larger market on other continents.
I would also add, that many ships of the line were built with a 20-30 year loan in mind, not 3-5 years, but if that is considered a reasonable term for profit, then you need to get cheaper transportation.
Alchemists have this same problem. When they reach above 10th level the goods they make move out of the price range of most noble shoppers.