While differences in cultural "expectations" might well have played a part vis-a-vis Knox in Perugia, I think the absolutely critical point here is this: things like intuition, profiling, phone tapping and so on can sometimes (maybe even often) be of real use in directing investigors towards specific individuals*.
BUT
That's all they can be. Of use in narrowing down the pool of potential suspects, and thus enabling investigators to focus their resources in a more optimal way.
What cannot and should not happen is that these kinds of "pointer" methods get magnified to being considered as evidence of guilt in and of themselves. Rather, it's then the job of investigators to go out and obtain real, hard, reliable, credible evidence. And it's only this actual evidence which should form the basis of any charging decision (and subsequent trial, if the decision is to charge).
I believe that the investigators in the Kercher murder case used methods that were probably deeply embedded in their overall approach and philosophy (and methods that, incidentally, were/are one of the very worst aspects of any inquisitorial criminal justice system). I believe that they were very well used to employing the following methodology:
1) Think of a wide selection of people who have potential links to the victim or the crime;
2) Examine each of those people in more detail. Are they unable to provide a provable alibi? Do they have potential motive? Do they have potential opportunity? Do they have potential means? Is their behaviour in front of investigators (or in phone taps) "strange" in some way?
3) If there are any people from the initial long list for whom the answer to all of the above questions is "yes", then it's probably they who committed the crime.
4) Now starts the task of finding the evidence to support the thesis that the persons(s) in (3) above did indeed commit the crime - this is where confirmation bias and tunnel vision on the part of the investigators can become a huge problem (as in the Knox/Sollecito investigation);
5) In conjunction with (4) above, the person(s) in question get brought in for interrogation, with the aim of extracting a useable (in court) confession. If they can manage to do this, it's solid gold (since the Italian courts historically treat all confessions as automatically reliable and credible....);
6) Once they have a confession, and a few pieces of supporting evidence (which, remember, may very well be the product of misinterpretation due to tunnel vision and/or confirmation bias), conviction is almost a formality.
And now, here's the thing: very often (in fact, probably almost always), this approach ends up with the investigators identifying the correct culprit, and the courts correctly convicting them. If, for example, a house is burgled, and the police recognise the MO as that of a recidivist burglar in their town, and the burglar cannot account for his movement around the time of the crime, and the burglar is nervous and evasive when police go round to talk with him.... well then, it's a pretty fair chance that this is the culprit. They may get the man to confess in a subsequent interrogation, and they may very well subsequently find corroborating physical evidence or witness testimony. And that evidence may well be enough, in totality, to see the man correctly convicted of the crime. And the investigators can slap themselves on the back for a) a job well done (the true culprit has been convicted and sentenced) and b) a vindication of their operating methods.
What appears to me to have happened in the Knox/Sollecito investigation is that they got to step (3) in my list above, and decided that:
a) Knox had to have been involved in some material way in the murder (though I think it's very clear that at that stage, they believed Knox had enabled (and subsequently covered up for) the actual murderer, rather than having directly participated in the attack herself);
b) by direct extension, Sollecito had to have, at the very least, lied to them about Knox's whereabouts on the night of the murder, and might also have had some sort of involvement in the murder itself;
c) therefore, both Knox and Sollecito had to have committed one or more serious criminal offences; and
d) Knox (and maybe also Sollecito) had to be able to tell them the identity of the man who had actually attacked and stabbed Kercher.
At that point, I think they crossed the Rubicon: they decided that their deductions were correct, and they set out to "prove" their deductions - first via forced confessions, and then via the (as they thought) inevitable physical evidence and witness testimony.
And the rest is (a very sorry) history........
* In the same way as, say, it's objectively more reasonable for security officials at airports to single out for enhanced searching a young man of Middle Eastern or South Asian ethnicity who's looking nervous and travelling alone.... as opposed to, say, a caucasian woman in her 50s who's travelling with her daughter and her daughter's two young children