Well, with Brian he was staging a suicide.
With Lila, he was in a hurry to kill her and get out of Paris.
Miguel was set up as a Skinner kill, who didn’t leave people naked.
And with Jordan, they didn’t have all supplies on hand and were in a hurry. I don’t remember if Dexter actually needled him, or just choked him out, but if he choked him they would have to strap him down quicker, which would cut out naked time. Or maybe the straps didn’t cover as much as the plastic wrap does and Lumen didn’t want to see his doodle *shrug*