What about this from Amanda's translation of part of the motivations? He at least addresses it here and goes on to assert that selective or not, someone cleaned up:
"it has been much discussed, especially by the defense of the defendants, whether a “selective” clean-up of the crime scene is possible by the authors of the crime. this possibility was denied on the basis of the empirical impossibility of a “naked eye” to identify and select the singular traces, often invisible, to destroy. it was also excluded that someone in the cottage of via della pergola, on the night between november 1st and 2nd, 2007, after having committed the murder of meredith kercher, could “selectively clean” the traces left by the authors of the crime, destroying all of the traces of the defendants in question, and leaving at the crime scene all of those traces that would have lead investigators to rudy hermann guede.
the affirmation, if apparently agreeable theoretically, must be correlated with the case in question, of which there are certain peculiarities.
it is peculiar, for example, that no traces of amanda marie knox were found in the cottage of via della pergola if not those which are refer-able to the murder – nor of raffaele sollecito. for the latter the explanation may be simple, that he had only just begun his sentimental relationship with amanda marie knox, and so had his patronage of her house, but regarding amanda marie knox the explanation is not simple at all, because she had been living there since the previous september.
the lack of biological traces of amanda marie knox at the cottage, if not those refer-able to the murder, is a circumstance that is surely singular and at the same time not easily explainable, if not with conjecture. but there are other examples, all of which have the same vulnus: to likely be conjecture.
the court retains that in fulfilling its duty, it must limit itself to a reasoning that is founded upon objective facts; upon that which emerged procedurally that are the most objective possible.
an argument characteristically objective that emerged procedurally was evidence that, after the murder of meredith kercher, selective or not, there was a clean-up of the traces of the murder, and a maneuvering of the body of poor meredith into a position (between the armoire and the wall of the room and covered by a duvet) that certainly doesn’t correspond with the position in which the girl died, at the end of the aggressive phase. someone spent much time within the cottage on the night between november 1st and 2nd, 2007, altering the crime scene and destroying numerous traces. the evidence provided by the scientific police proves this incontestable truth, which the court’s reasoning must take into consideration."
ETA (added quotes around Nencini's motivation copied from AK's website)