I’m probably not on the same end of the political spectrum as you, but agree with most of what you say. The will of the people should be paramount.
Two points though: any system has to allow for the will of the people to change, especially when referendum results have been close. One can argue about how often that should be measured, or how big a “material change” has to be, but the key point is that the will of the people changes over time and referenda results - and for that matter, election results - cannot be regarded as answering questions for all time or in all circumstances.
Secondly, the prevailing political philosophy in Scotland evolved differently from that in England. In Scotland, the concept that sovereignty rests with the people has been embedded for centuries. In England, sovereignty rests with the crown in parliament, a pretty daft concept in the 21st century. The Scottish approach seems far more in line with your world view.
And if the will of the people is paramount, why not the will of the Scottish people? Why do we need to align ourselves to any neighbour - meaning, of course, they make all our most important decisions for us? No other country in the world is trying to do that.
After independence, everything will stay exactly the same - except the power to change everything.