My guess is that the ether jet and the parasites were chosen because of their extremely useful properties that very few other ships have. This way, if you want to take advantage of those mechanics, but you don't want to use your first bonus ship type on it (the one you selected on the map screen) you can still do so, for a very steep premium of course.
Similar reasoning for the enclave, except it is to save on knowledge for a premium on price.
Not sure about why the beam frigate was chosen to be "merced" though. I gotta say though, Mk. IV beam frigates do indeed ROCK!