There are some cases where a ship generated in the ship market can be very powerful, and sometimes the ship generated can just be so-so. Some combos generated would be very expensive to create using upgrades. I've seen some pretty nasty ships get generated through this thing. But like real life, not every vehicle can be a Rolls Royce.
A combo with very high stats in multiple areas is pretty rare, but some ships rarely come with special abilities that can't be bought through upgrades.
It has to be balanced pretty carefully to keep from rendering the upgrade ship feature of the game basically useless.