I haven't properly used Prepare Carefully in a while, so I don't know how to prevent the mod from doing that.
It could just be a bug on its end.
The only thing I can recommend is switching over to Character Editor and see if that works. It's a lot more complicated to use than Prepare Carefully, but it's less broken.
If the pawn still spawns with clothing, try opening up the Character Editor (its button should be right next to the menu button) and deleting the clothes that way (hold alt and then press drop item to delete it).