From what I saw in the gameplay they can be positioned anywhere as long as they counter-weight the ship. So asymmetrical placements don’t SEEM like they’ll screw up your ship if one goes blarg, you could always do your stern-and-bow idea with extra stones in the hull anyway, that might make the visible stones more of amplification devices.
The reasons for changing to a single core was because multiple cores were almost consequence-free in terms of ship design. Just slap ’em anywhere with little planning or thought.
Now that ships can only have one core, it does limit the designs and sizes initially – but as more upgrades are added and better quality core/parts researched, I’m sure that restriction will evaporate and players will be able to achieve larger ships. Then it becomes a reward for exploring the world. It becomes a more structured form of player progression. You can’t start out building huge ships in the first 5 minutes, but most instead work towards that goal.