There's three major advantages to having the engines in the back:

1. The Engine truss provides a convenient structural carrying element for stacking stages, since the engines need to a structural truss to attach too anyway.

2. Because acceleration from the engine causes the fuel to pool at the rear end of the tank, the fuel outlet has to be there. Engines in the back means both less head required for the turbopumps, since they are aided by the acceleration of the vehicle, rather than having to suck fuel against it. For the same reasom they'd also be much less prone to fuel cavitation. And lastly the engines being close to the fuel outlet obviously means significantly shorter feed lines.

3. Not blasting hot exhaust gases past/against your big tank of explosive fuels.

All 3 points are most crucial for chemical high thrust engines. For things like ion drives they are less relevant.