The whole timeline begins on a lie on their part - that Jonbenet was asleep & carried up to bed - LIE! Johns himself later contradicts himself, Burke says she was awake...and she had pineapple which had been eaten a few hours before death. Now, if I remember right there is at least one person who thinks an intruder her gave her a nice little snack.....which I thought was some sort of ironic joke at the time but....it wasn't.
You know the IDI would be plausible IF the evidence added up that way...the evidence individually & collectively points to the R.s (yes, yes, there is the holy DNA - as I said if someone helped them that explains that, & many other explainations which have already been posted explains that, too.).
Intruders take the body - maybe the body is later found, maybe not. Maybe there are clues, maybe not (Polly Klass, Danielle VanDamm, etc). But, they do NOT hang around a house...have snacks, write long 'ransom' notes in the office, & after 'botching up' the kidnap & apparently being in a quandry of what to do/how to kill her but manage to many times over, when she's dead redress her & tape her up...cause maybe they'll take, but no, they then they decide they won't...and finally leave the body where there could be evidence linking them instead of taking & disposing (and isn't it amazing that aside from the 'touch' DNA there is NO evidence..oh, right, aside from the Ramseys).....
I think they had intended on taking Jonbenet's body out of the house & to Atlanta & dispose of it...the actually thought they could leave & wanted to - real concerned parents there. When they realized they weren't going anywhere...John 'discovers' the body....