The main threat of safety is when you start operating outside of your Aircraft State of Registry laws / ANO etc. This will inevitably lead to more incidents and accidents and be a less safe operation. There have been many Operators over the years where this has indeed caused safety incidents - operating outside of their State of Registry legally binding rules, therefore essentially uninsurable as a result.
Part-NCC and the rest of Regulation 965/2012 for EASA Air Operations is the law in all EU member states, in the same way Part-CAT is for AOC operators. It automatically superceeds and overrides all equivalent legislation at national level. The ANO in the UK will be updated in 2016 to reflect this when NCO/NCC comes into force. There isn't really any question over its legal status.
Inevitably there is a bit of confusion over practical implementation at the outset with all regulations, especially when it's being applied to operators for whom formal organisational requirements are something new. The UK CAA has put a certain amount of effort into explaining the new rules, although I don't know how effective that has been.
That all said, Part-NCC asks for requirements well over the top of current national regulations for privately operated complex aircraft, which generally already had a reasonable safety record - I'd be amazed if it does much to improve it! Classic case of a solution in search of a problem if you ask me.