You have made good points here. Also, on IIP, poster Katody has pointed out that the CPP Art. 620 para. 1a is only meant to apply to charge B, carrying the knife.
I believe that is a reasonable and conservative view of what the CSC intended here. I may have overreached in thinking ("momentarily") that the initial CPP Art. 620 para. 1a reference applied to the whole despositivo.
Also, CP Art. 61 para. 2 only applies to aggravating circumstances in general:
Source:
http://www.diritto.it/codici/articolo/4281113-codice-penale-circostanze-aggravanti-comuni
Google translated
So indeed, I would agree that CPP Art. 620 para. 1L and CPP Art. 530 para. 2 must be referring specifically to the aggravating circumstances of the calunnia charge. The aggravating circumstances would only make sense if Amanda Knox were guilty of the murder or some other crime, so CP Art. 61 cannot remain.
This leaves a little mystery about the rest of the charges. The terminology "the accused did not commit it {the criminal act}" is found in CPP Art. 530 para. 1. So that would seem to be applied to charges A, D, and F, but there is ambiguity, as you point out. It could be that CPP Art. 530 para. 2 from the previous clause is meant to apply. I suggest that there is no real difference, in the sense that "insufficient evidence" includes "no reliable evidence of guilt" and that because of the presumption of innocence, any acquittal based on defects in evidence (including no reliable evidence) must mean that legally the criminal act was not committed by the accused.
We need to see the Marasca CSC panel motivation report to more fully understand the reasoning. They may decide not to mention the procedural law violations in order to save face or avoid conflict. The Hellmann court MR did not explicitly state that there were procedural law violations, although it came close in its statements about the Nov. 5/6 interrogation of Amanda Knox.
Thanks for your post, which has helped clarify the meaning of the dispositivo.