Well there is the issue that putting her in the trunk removed any element of denial if she were discovered. That's the reason people argue John 'found' her, realizing if he didn't do it then, it was going to be hard to explain why he hadn't looked very hard when the police or the friend inevitably found her. Finding her in the house looked bad enough, but finding her in John's trunk would point the finger right at him. Under that theory, he didn't expect police to find her, until the police detective didn't leave and told everyone to search. So that would indicate he did intend to move her. I don't know why everyone being up was the issue - if Patsy was allegedly in on it, it didn't matter. If she wasn't, I'm sure he could have distracted her. And it would be easy to hide the transfer from Burke, especially if both parents were in on it. The police are the problem, not the family.
A crime scene would be searched - that's what I mean. The police weren't focused on the house as the crime scene at that point. They were, however, expecting the kidnapper to try and make contact, so yes, they would be monitoring communications and John's comings and goings related to the money. Maybe monitoring the house, but not necessarily - a kidnapper doesn't usually come back, unless that's where he wants to do the hand off. I agree that it would have been very hard for John to not be seen disposing of a body because police would want to tail him everywhere, which is where the scenario kind of falls apart. It's not a great scenario by any means. But it is more logical to me than any other one, because, as you said, there is no point to the note if there wasn't some plan to remove her, but there's also no point to the intruder doing it.