I think your summary covers things well. It is up to each State to implement whichever bits of ICAO they choose to in the best way that fits the legal framework. In theory each State should do all of ICAO if it can but many file Differences for reasons related to national policy or perhaps even not wanting to change something that works and is well understood.
For all the flaws in the ICAO system, the SARPs etc are generally consistent with each other. This means that if a State deviates from or does not apply one SARP or PANS it is common for problems to be created elsewhere because something that was assumed to be in place is not. The UK has had a tendency in the past to do some things in its own way - sometimes with very good and justifiable reasons in my personal view - but it does mean that it sometimes has to find more and more fixes for a problem which wouldn't even exist if they'd just applied the ICAO rules.
However, the UK has a very good set of national and local procedure manuals that describe in a lot of detail how ATC should be done - I don't know if you have the same in Italy. If a controller follows the procedures in the manuals this will usually be a good enough defence if something goes wrong like Cagliari. The people who write the manuals and oversee them (the NSA) would probably also have to justify why they considered the procedures to be adequate also. Unless the controller can be shown to have been actively negligent I would hope that he/she would not be convicted in court (but, of course, you can never be sure what a court will conclude). Again, I don't know how the Italian legal system works so I've no idea whether there are parallels with the UK.
I agree with you that the considerations set out in PANS-ATM for applying reduced runway separation now are better than for the previous land after procedures. As I said, I can't see why the UK national procedures have not been updated - only the people who write the procedures (in the CAA) can tell us. But even if the books had been updated, a controller has options about which procedures he/she uses - if you don't feel that using reduced runway separation is a good idea in a particular situation, then don't use it. I sometimes hear these sort of decisions being described as defensive controlling and it does appear to be quite common in some places that I have seen - perhaps because of legal decisions that have been made.
In some ways the situation may get easier before too long because EASA is planning to introduce regulations about rules of the air and ATC procedures - effectively mandating ICAO Annex 2 and PANS-ATM. This will mean, in theory anyway, that States cannot file individual Differences and we will all do ATC in the same way across the whole of Europe. What will happen in practice, is another 'who knows'!