This is what's always so difficult when discussing cases like this: you have one side saying one thing (the debris in the window well was never disturbed) and another saying another (it was). I've heard both too, so I certainly don't blame you for believing this. Same thing about the foot-print marks in the snow.
But with regard to the scuff mark on the wall, this is clear: JR admitted to breaking that very window himself, and climbing through that very window, (months I want to say) before the murder took place -- and he never bothered to fix it. So obviously, the scuff mark could have very easily come from him as he slid down the wall and into the train room (if you look at the mark, to me, it looks like it has a downward trajectory, rather than upward).
With regard to the "high-tek" boot mark, again, I've heard two things: that no one in the house ever owned a pair of those boots, and that BR himself owned a pair. So again, it's one of those "which side to believe" things, because I've seen this reported by more "reliable" sources (television specials), i.e. not just on the internet and/or on message boards.
I do agree that the unidentified DNA underneath her fingernails is relevant and suspicious. I am a RDI'er, mostly PDI'er, but this is a factor I can't simply dismiss outright like many can (which is fine, I'm just saying). I can dismiss the touch DNA "evidence" because touch DNA isn't strong enough -- everything has touch DNA -- but the DNA underneath her fingernails is the one thing that gives me pause.
The thing is, John admitted coming through that window whilst wearing his black dress shoes several months prior, so the debris certainly would be disturbed and it would also explain the marks on the wall. If you look at the whole thing objectively, taking in to account that John never even mentioned the window being opened until three months later, and the untouched spiderweb, It becomes fairly clear that it is very unlikely that someone came through that window.
Yes it was reported that the Ramsey's didn't own HiTek boots, they said so many times on national TV. Thats what people remember. What didn't make it on TV very much on TV was Fleet White's statement that he knows for sure that Burke had HiTek boots with a compass on the laces because he'd seen them in his own home.
As far as DNA, you've had the wool pulled over your eyes. Everybody has other peoples DNA on them, especially children. There is no way to time stamp the DNA under her nails so it is very probable that the DNA under her nails had nothing to do with the crime. The Ramsey team was clever, using the media to hammer home things that they knew had nothing to do with the crime, trying to link it to a fictional intruder. Animal hair anyone? Must be from the intruder. Pineapple? Not ours. Flashlight? What flashlight. It goes on and on, lie after lie.