Ships don't have to be given the exact same stats as living characters, that's a pretty poor argument.
Having ships function like characters doesn't mean they are characters. I don't see a good argument against this.
In fact I don't see good arguments against starship rules presented thus far. The Fate fractal seems to be the way to go, or something like it. Even though the Cortex+ system is a bit convoluted, it deals with ships well in a similar fashion.
It makes sense for them to use the same mechanics with comparable stats to the PC's because it's simpler, rather than suddenly switching to a compeltely different system fo the sake of simulation, perhaps, when flying.