The difference is a matter of principle, as I haven’t advocated for nationalism, but the principles that I just cited. If those principles coincidentally align with nationalism, then it’s a boon to the nationalists, I suppose, but logic does not hold that you can accuse someone of advocating nationalism based on such a coincidence.
If the people of Scotland who favor independence are voting to depart to protect their rights as individuals (which I doubt), I am with them. If they are voting merely to be governed by people arbitrarily born in Scotland rather than by people arbitrarily born in Scotland, England, Wales and Northern Ireland, I see no moral justification for that, especially if the new Scottish government will use that power to further violate their rights (which is what I think will happen).
The sovereign is a means, not an end. Always.