I see the note as being an effort to cover up the crime not that the killer really wanted the money.
To cover up the crime the note delays a murder investigation.
A missing child is looked for in every nook and cranny in the house around the house in the neighborhood. After all she could have just wandered off.
A ransom note tells people don't look as she is with me. When looking does happen it is looking for points of entry how the kidnapper got in. The wine cellar didn't seem important to people looking for points of entry even a cursory look would have noticed how dark the room is and the person would assume no windows here forget this room. The attention would have been drawn up and away from the floor to anyone looking for windows or other types of entry.
Once the body leaves the house any perp takes a bigger risk of being seen when body is dumped. They also risk leaving more forensic clues like fibers from their car. Johns car fibers are easy to explain. She rode in it on the way home fibers could be anywhere on her and she could have transferred them herself. Started out on hair rubbed off on nightgown while sleeping. All the fiber evidence used in the RDI theories from her home, parents, etc. would be expected to be found on her. They would be less damming and more likely gone if her body was dumped remotely. IMO it serves the parents to get her out of the house more than it serves an intruder.
What gives me pause is the rope. I have never bought rope that wasn't packaged in at least a 10 foot piece. Even rope for a clothes line is at least 10 ft long. How many feet of rope was found along with her body? I bet one end had been cut and some of the rope is missing. Not in their house, boat, or second house was any of this rope found. Why would police look for additional pieces of the rope if it was complete with factory sealed ends to prevent ravel present.