You are twisting this. Yes, Guede's trial came to the conclusion that he did not act alone. But it is AK & RS trial that came to the conclusion that they are the ones who acted with Guede.
Guede's "trial" was a fast track trial, meaning that it is the regular process with the "trial phase" missing. The trial phase is the part of the trial where evidence is evaluated. Therefore the court was drawing conclusion from only uncontested claims made by the prosecution, not because evidence was presented.
In exchange for certain admissions, a defendant foregoes a trial phase. Therefore all the "conclusions" which such a process draws are ones that noth sides, prosecution and defence (in this case Rudy's defence) simply agree upon.
Both sides said that Rudy did not act alone. No evidence was presented to either prove or disprove this. Such evidence would be part of a trial-phase which in a fast-track is, as stated, missing.
Furthermore, as mentioned upthread the Borsini motivations report is the one which says:
"Then, apart from the attempt to staunch the flow of blood from the wound and the proof that it was not he that held the knife that was compatible with the worst of the lesions, it should also be remembered that Guede was the only one, even if in a somewhat fanciful reconstruction of events, to indicate the perpetrators."
My reading of this is that it is not "the evidence" per se that indicates who those other perpetrators are, it is Rudy Guede himself, who has tremendous incentive to name Knox and Sollecito to get mitigation for his sentence.
Which is, in fact, what happened.
Now in the Nencini report, which you have read in the original Italian, Rudy becomes to sole source of motive - that Meredith and Amanda were fighting over rent money. And this is cherry-picked by Nencini from a set of ever changing "admissions" from Guede, this one though is from an admission where Rudy specifically says that Meredith let him into the cottage (not Amanda), and the Meredith searched Amanda's room for the rent money, meaning that Amanda was not there.
So you are right - Guede's trial did come to the conclusion that he did not act alone - and this was at a process where no evidence at all was submitted (not could it be because of the missing trial phase) that shows that he obviously did act alone. And Borsini's comments, acc. to the ISC, now lock Amanda and Raffaele's process into finding that they are the others.
Nencini's report shows the ridiculousness of trying to harmonize Rudy's process with Amanda's and Raffaele's. Nencini has to claim all those ridiculous things you have read in the original Italian, but will not even comment upon.
All to harmonize according to the ISC instructions, that Rudy's trial process is to be preferred.