How do airliners with engines mounted on places other than wings suppress wing flutter?
Since flutter is a natural-frequency harmonics phenomenon, it's a matter of "tuning" the wing box structure with the required stiffness and damping to move its natural frequency range outside the range experienced with its C of G and torsional center offset and uncompensated for with engines on pylons.

It's a bit like with flight controls.  With manual ailerons, the aileron/wing system is flexible you could say, and needs mass balancing.  Like wing mounted engines.   

With hydraulic controls, the connection between the aileron and wing is rigid outside of movement induced by the hydraulic actuator.  No mass balance required.  Like a wing box with no engines that has to be inherently stiffer than otherwise.

It's one reason wing mounted engines are more common than tail mounted.  Lets you make the wing box structure a little lighter.