Well, duh. If you can't spot the differences between urban vs rural and, as an example, Georgian vs Abkhazian, you need to read up.
The Abkhazians consider themselves a distinct ethnic group from the Georgians, while both sides of the rural-urban and east-west-north-south divides consider themselves part of the same ethnic group. Urban and rural groups of the same ethnicity tend to view themselves as different parts of the same organism. Different ethnic groups tend to view each other as separate organisms.
Just look to what actually happens in practice to see that there is a difference: I can't think of any country that split into Urbanistan and Ruralistan. Northistan and Southistan is more likely, but not so likely without considerable cultural differences (and there does seem to be considerable cultural differences within the US).
In part, the difference is qualitative: Identity versus ideology.
In part it is quantitative: not many people will seriously support autonomy without some concept of differing ethnic identities. Many Scots will vote in favour of secession, but if you pick an area within Scotland and ask if it should secede from the rest of Scotland, the amount of serious support in most cases (perhaps all, I don't know Scotland well enough) would drop to near zero.
Once the cultural differences reach a certain point (like languages that are not mutually intelligible), I think a great deal of serious support for separatism is always going to be present, even if most of it may lay dormant.
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