It's true, I don't believe Amanda convinced her boyfriend of 5 days to kill the only native English speaker she was friends with for no reason and on a night they previously had other engagements on they spontaneously recruited a local burglar they just happened by sheer chance to run into to come along and help kill, within a 20 minute time span, and when all was said and done the crime scene resembled a break-in that was forensically and idiosyncratically similar to this burglar's previous break-in with a murder victim surrounded by the burglar's bloody prints and DNA. It's a non sequitur crime and frankly it really doesn't matter to me what the evidence is.
It makes no sense. You can't investigate a crime starting from a pre-set scenario.
That would be pure circular fallacy. If you assume a working scenario that is nonsense by your own definition, then by definition you state and conclude that the crime makes no sense.
You need to start from evidence.
The alleged break in is not similar to the previous which is putatively attributed to tha individual (who has no precedent for burglary btw).
That one was from a balcony this one is from a window. In that one items and values were taken and drawers searched, in this one they were not, instead usless item were strawn around.
But in fact the alleged burglary does not look like a burglary at all. It looks like a staging, which is something very common on house murders.
The point of entry is illogical, there is an extremely easy and safe way in on the rear of the house, repaired from view; statistics moreover show that almost all burglaries chose either ground floor or balconies; that entrance from wall climbing instead is difficult and hazardous, and exposed to view from road and parking a few meters away. Burglars just don't take such useless risks, especially when they have a balcony on the rear.
There is no soil inside the room (dark soil from the garden below);
there are no soeprints on the grass and on the earth below the window;
first thing buglaries do is search through drawers, and drawers in the house were not searched;
clothes and items of no interest for a burglar were taken from the wardrobe and scattered around the room: it makes no sense for a true thief;
there is no DNA and no fingerprints of the alleged burglar in the room;
only one room has traces of such apparent "search" by a burglar; but do usually burglars search one room only?
In that room, here is instead, surprisingly, a mixed trace of Meredith + Knox on two spots of luminol stains where there is no reason for DNA of such people to be there;
the glass shards on the window sill were not touched by the "burglar";
small and transportable values like jewels were not taken: how is it possible that he got interrupted so "early" to the point of not even searching drawers or take small values?
on a logical point of view, a burglar doesn't have a motive to commit rape, you can't deduce one thing from another; (there is no evidence Guede committed the a burglary anyway);
there are obvious physical traces of two different
modus operandi on the scene, forming two sets of evidence, a series of dycothomies (some perpetrator was barefoot and walked with bare feet in bloody water, some other had shoes, for example);
the autopsy report, crossed with physical findings in the room, shows multiple perpetrators;
physical traces such as isolation of bathmat prints, shoeprints over alleged semen stain, trail of shoeprints not turning towards the door (which was locked instead) make it impossible to think about a lone perpetrator dynamic; think about the steps on semen stain on the pillow for example: you "placed" the victim on the pillow when she is already dying (instead you would require normal blood pressure to produce bruises), and then in your scenario the raper ejaculates on the pillow when the body is already lyin on it: but at that point, how could the murderer step on the pillow?
This is just to start, to see how looking at the evidence looks like.
