I'm speculating here, but judging solely by the UI, you would be bound by the current population distribution of the combined counties at the time you claim them. On the D&SS map, the "claim" button exists at each tier.
So the question is which happens first? Claiming the settlement or claiming the county? If you claim a county first, then how you impact the population of your settlement won't matter, and frankly, it seems like it should.
In the live stream, they said they were deliberately leaving the claiming process vague so we would discover how it worked once D&SS resumes. If we don't get clarification, I'd suggest just having a plan A and a plan B and then having your duke explain the selection sequence to you as well as the affect on population distribution, since they will be claiming long before you will.