About percentages at a referendum, the cleanest approach would be that at least 50% of the total electorate would have to have chosen for one of the two options. That way you could actually state that the will of the people is X. It would be quite hard for either option to reach that point, though.
Moreover, any of this tinkering with percentages doesn't solve the problem of binary referenda not giving a clear answer about what people DO want. They often only tell you what they DON'T want. The Brexit referendum is a case in point. 51.9% of the voters in a 72.2% turnout wanted to leave the EU. The problem that we are now facing is that there is no idea about what they want to happen after the UK has left. SM+CU? Hard Brexit? Something in between? If that was crystal clear then the country wouldn't be in the mess it is in now.
I think the most popular way to leave the EU would perhaps get support by 30% of the population, that means that 70% would be unhappy. And that is the most popular one, we're more likely to end up in a scenario that only 15% would support, making the other 85% unhappy. That is why the country is currently ungovernable and another referendum or general election won't make that go away. We'll be discussing Brexit for at least another decade before we get any closure.