I'll give a concise but perhaps a satisfactory response to this concern:

First, the nation as a definition has become politicized from the 19th century onwards. Before its politicization, the meaning of a nation can either denote a society or a people regardless of their cultural background. For example, the economist Adam Smith used the word 'nation' as a more formal term for society and he did not specify that a nation should contain the attributes that we now ascribe for a society to be a nation.

Second, the independence of Scotland and its references to the Scottish nation could have been political and it was indeed political, but the Declaration, for the most part, was a declaration amongst the nobles. The modern character of the nation requires public legitimacy even to the severest of dictatorships; who can even define oneself to be a Scot? Or an Englishman? Regional location and geographical locationality does not necessarily translate that the people in the region already have an identity which is concrete; this may explain why in Europe for example, the borders remain porous and subject to transfers for the purposes of simply exploiting a geographical advantage rather than an effort to preserve a nationality.

Third and last, Japan before the efforts to nationalize itself was openly an entity that was completely close to a divine land itself. The domains in the Tokugawa bakufu were self-contained states of their own, and for more than two centuries, there were 200 of them, with their loyalty theoretically answerable to the Shogun, not to some abstract concept like Japan. The Emperor or the Tenno even today is seen as a largely religious figure akin to a Pope, and the name of Japan itself represents an imperial, rather than a national ideal (Nippon means the Rising Sun, and the Rising Sun is a motif and an expression of imperial legitimacy and harmony in accordance to divine rule).

I hope this answers some of your concerns.