IMO - A teleportation device should not have had enough power to breakdown DD and teleport him. .
Lifting a bicycle isn't the same as lifting a car.
Tearing 5 pages isn't the same as tearing a 500 page book.
Breaking down a vulnerable human on the molecular level via a teleportation device should not be the same as breaking down and reconstructing an invulnerable DD. If this was the case, why not just build a nice handy little teleporter gun which doesn't do the reconstructing part.
With that said, DD resists the void and jumps in and negates him like he did the radiant.