Playing devils advocate. Why wipe the flashlight and batteries set it neatly back on the table? Why not pull an OJ throw all that stuff in a duffle Bag and get rid off it and all the other small items like PR paintbrush. It's not like a door knob or permanent fixture you can wipe down but can't take and hide. The house was 7,500sq ft I'm sure they could have gotten rid or hide all the evidence that points to them.
To be honest I think "why was JonBenet's body still in the house" is a much bigger question and the flashlight's presence pales in comparison.
If it wasn't snowing, then why not drive off somewhere and put the body in woods and make it look like a real abduction to match the note?
Did Burke get up too early and changed the plans so that the police call had to be made immediately instead of a few hours later?
Only another forensic examination of the flashlight could confirm without doubt that the flashlight and batteries were wiped down. If they were wiped clean, then that strongly suggests that the Ramseys thought it was what was used. If it wasn't actually wiped clean, then that's something different.
Batteries (or is it lightbulbs?) shouldn't be touched when inserting them as that's supposed to affect their lifespan...some people would naturally try to insert batteries with a little finger contact as possible for that reason. No fingerprints on a flashlight casing is a bigger mystery...the batteries could be irrelevant.
I think the pineapple is very easily explained, because the focus of the cover up would be on the body, the room it's present in (but not what seem like minor details of the room, the fact that it's a room in active use, which anyone doing a cover up might want to leave intact to show that it's just a normal family room that nothing untoward has happened in), so I'm saying simply move the body and scene of crime elsewhere and focus on that place and scenesetting for the place where the body will be discovered.
There's only a few grief-stricken hours in which to do all of this. The pen was returned, the notepad returned, the indented pages were still present on the notepad. These are the actions of someone not thinking clearly and acting on automatic. There could be a ridiculous reason like wanting to use the flashlight to search in the dark....things don't always make perfect sense in real life because, unlike when writing a book, you don't have months to think about ever detail, and when overwhelmed with emotion you make strange errors by doing thing on automatic ...like putting the pen and notepad back in their home where they belong because it's the ransom note that matters and which you want to be found.
I think half the reason why this show is such an eye-opener is that it's not focused on every tiny detail. And that is actually good detective work...getting lost in details that have no logical explanation, because they are not the result of a clear-thinking mind, can be a massive error.