Luthiers frequently cite: The main disadvantage is relatively complex construction that leads to higher manufacturing and servicing costs.
Another cited disadvantage is the inability or relative complexity of adding a double-locking tremolo to the guitar, as the routing for cavities would interfere with deeply set neck.
David Thomas McNaught claims to be the first who proposed a modern version of set-through neck joint.
Usually, it's hard to determine if the guitar has set-through neck or neck-through body judging only the general outlook.
Rich's Invisibolt Technology is one notable exception that uses black ("shadow") body and contrasting light neck wood.