If it were so easy just better refine the fuel why would Europeans bother to add these converters and adblue injectors? No it's not impurities, but high pressure/temperature combustion. The higher the more efficient and more NOx comes out.
However, it's not insane to look at what experts put in place and consider that there are reasons why they have done that. Yes, experts can be wrong or are forced to make sub-optimal decisions, but it's worth examining their thinking behind the decisions.
In theory, yes. In practise, the experts will also consider real-world constraints (e.g. cost, planning, staffing etc). Also, taking the advice/opinion of respected experts (i.e. not YouTube experts) is a short-cut to spending years studying the science (that they had to do) yourself and that's even assuming that you can reach the same level of competency as them.
Fuel NOx is only one of them, which you quite rightly point out is not dominant in methane combustion due to the rarity of nitrogen in the fuel.
The dominant source in methane combustion is thermal NOx, which forms due to the extreme temperature of the combustion, causing atmospheric nitrogen to decompose and react with atmospheric oxygen.
It's impurities in oxidizer. 80% of air is N2, 20% O2. N2 + O2 -> NOx minus some kJ(endothermic). Means, run plain air through anything hot and NOx comes out. Doesn't matter how pure the fuel, doesn't have to be an ICE, doesn't need fuel at all. Hot stuff in the air = NOx.
