[AZLiberty]

It depends on the builder.

Some builders (e.g. Larrivee) relocate the bridge downward to accommodate the shorter neck on a 12 fret. Since the bridge is in a different location the guitar is necessarily "voiced" differently.

Other builders (e.g. Martin) use a different body shape which is longer for their 12-fret instruments. Thus the guitar sounds different because the body is shaped differently.