Economies of scale wouldn't result in any big jump in price, and they could slightly lessen the numbers easily to make up for it. (Most people do not own two of each Large ship, for instance.)
In exchange, they have a real Conversion Kit, where customers can actually buy -- or trade -- for the number of ships they want and need to convert.
Y'all can speculate about how upset people would be to have redundant cardboard, but it always seems to ignore that the "redundant" cardboard would actually have easily-realized value. Under the scheme they have chosen, it does not.
What FFG has chosen to do is make it very difficult for all of their 1.0 customers to make use of all of a Conversion Kit. Whether they've done that deliberately (in a misguided attempt to sell more CKs) or out of ignorance, I don't really know, but it is going to result in a huge amount of unused and unusable extra cardboard, and a good number of disgruntled players ... and both of those could have been avoided.
But apologists gonna apologist.