One of the mysteries in general aviation is that twin engine airplanes have more accidents than singles. One of the factors is asymmetrical thrust after an engine failure. As such, centerline thrust is considered to be a virtue because pilots have an easier time with it. It also allows all the engine's power to be used for thrust, instead of wasting some on rudder.
So the closer to centerline the engine is, the easier it is on the pilot.
However, the nature of propellers makes it difficult to put two propellers on centerline. You either need a "pod" fuselage with a twin tail, like a Skymaster... or stacked contra-rotating props with one engine per prop. Of course, the trend toward electric props is going to improve that, allowing prop placement now not possible.
Of course in complex aircraft and jetliners, the autopilots relieve much of the workload and opportunity for error. Those will usually be there to assist, because there's little chance of those automated systems also failing at the same time. That reduces the safety impact of widely separated engines.