Scotland is a much more well defined and homogeneous nation than most European nations. The old highland/lowland dividing line is virtually obsolete as the Gaeliec culture has in reality died out outside of the Western Isles (highland (pseudo-)culture has of course on a symbolic level spread to all of Scotland in the form of kilts, bagpipes and tartans etc.).
Uh-oh, sounds like someone needs to read up on his Eric Hobsbawn!
I understand your points and they're well-taken, but ultimately I think any areas of Scotland that genuinely would prefer to stay in the UK by large margins should be allowed to if they make their wishes clear. There's something disturbing to me about saying, well they have to leave the UK no matter what their wishes because that's the collective will of ~the nation~. It sounds very early 20th century to me.
So you suggest that Scotland should look like a Swiss Cheese with every household deciding whether they want to be part of UK or Scotland, in fact that does seem a little unfair, what about households, where people vote for two different sides, I think we should split them or make them co-domains of Scotland and UK. Clearly that would be the anti-nationalist solution. In fact I think we should extent this to the general vote, with households voting for one party, getting their candidate as PM, while household voting for the other party getting their candidate as PM.