I hate to be "That guy", but when it comes to such designs of space ship, it really depends on what the engine is ultimately handling for the ship. If it handles shields as well(hypothetically), then it's at the most ideal spot.
Non-flammable fuel types would also ideally be placed near the cockpit. I see that it has guest/prisoner quarters, so you definitely don't want to have to pass passengers to reach said engine room. And you don't want people messing with your engines and not know first.(of course, fixed with cameras).
If it's a radiation risk, the core can be scrammed downwards.
If it is handling the artificial gravity, near center is probably best, too, or else the effect is greater at one end and weak toward the other, canceling propulsion/braking.
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