Well, I know for the Legacy and Starter packs, it gives you all the boxen right up front, so you'd be getting a VAdm ship at level 1. I'm sure the game engine would be very Not Happy about that sort of thing. A box seems like the existing solution.
I believe they do this to avoid complications if you have no empty ship slots. Like if you try to open the box it just tells you that you have no slots free for it, but the box in your inventory proves that you did actually purchase it and that there isn't an error with the C-store maybe? I suppose they could make it so that you just can't claim it from the C-store if you have no empty slots, but I don't know how their system really works. That's really the best answer I can think of. Other than that I don't know lol.