The relevant paragraph of Art 104 is as follows:
3. Nel corso delle indagini preliminari, quando sussistono specifiche ed eccezionali ragioni di cautela, il giudice su richiesta del pubblico ministero può, con decreto motivato, dilazionare, per un tempo non superiore a cinque giorni, l'esercizio del diritto di conferire con il difensore.
3. In the course of the preliminary investigation, where there are specific and exceptional reasons of caution, the judge at the request of the public prosecutor may, by reasoned decree, defer, for a period not exceeding five days, the exercising of the right to confer with the defendant.
Note the words specific and exceptional. Unfortunately, while they have obvious meaning, they are sufficiently nebulous and subjective as to allow egregious misapplication.
By any reasonable, objective measure, the circumstances surrounding the detention of Knox, Sollecito and Lumumba cannot be described as "specific and exceptional". There can be no possibility of a wider criminal conspiracy - indeed, the police and PM firmly believed that they had identified and arrested all three perpetrators at that point. And there is of course no evidence whatsoever to suppose that had Knox and Sollecito (and Lumumba) been properly provided with access to legal counsel, this could/would in any way have jeopardised the investigation or the prospects of conviction.
Simply put, this section of the code was grossly abused by Mignini in this case, and he was ably abetted by the investigating judge. I have little doubt that the ECHR will interpret things in this manner also.
The ECHR is highly likely to say, well you can keep"specific and exceptional" suspects from seeing attorneys for up to 5 days, but anything any suspects say or write during that period without counsel cannot be used in court against them. ECHR actually would find 5 days too long a period to keep a suspect from an attorney, IIUC. And as you write, Knox, Sollecito, and Lumumba would not be "exceptional" in the apparent sense of linkage to a crime or terrorist organization. ECHR doesn't support arbitrary detention or arbitrary denial of counsel.