One of the best parts of the whole Kent section in P&P to me is trying to guess at what Darcy is thinking based on the hints that Austen gives us. When he first arrives, he shows up at the parsonage immediately, which we take to mean that he is eager to see Elizabeth again. I've always thought that maybe he was hoping to find her not as attractive as he remembered, which would let him finally get over her. Either way, he ignores them for the rest of the week, which suggests that he has decided that his only recourse is to stay away from her. The change occurs on Easter Sunday evening, when after an evening of watching Elizabeth talk to his cousin he finally gives up and goes over to her, and they flirt over the piano. The very next day he shows up at the parsonage with marriage on his mind. How do we know he has marriage on his mind? We can reasonably infer it based on the fact that he is wondering whether she would mind living a long way from Longbourn. You're right in that these comments appear somewhat contradictory, but they both show his mind tending in the same direction. In the first, he's trying to argue with her that her idea of "far" is not really a reasonable one. It only seems far to her because she has so little experience of travel. (Ergo, Pemberley is not really as far from Longbourn as it might seem to her now.) In the second, he's arguing that she surely can't be that attached to her home anyway. So--it's not that far, and you surely wouldn't really mind leaving. I agree with others that he might have thought she must have lived somewhere besides Longbourn because he can't otherwise explain why she is so different from most of her family. It was not at all uncommon for children to be sent to live with other family members at that time, particularly in a large household, or he might have thought she had gone away to school somewhere.
I don't think that Darcy was trying to make a systematic, carefully organized argument here. I think he was distracted, trying not to show how much her presence affected him, plus he was so busy thinking about the whole marriage idea that he's not paying as much attention to the conversation as he might have been. So in a sense, his comments are disconnected and a bit random, but they reveal to the reader (though not to Elizabeth) the direction of his thoughts. They're kind of similar to the "series of odd, disconnected questions" that he kept asking during their walks--questions that, while they meant nothing to her, carry a great deal of potential significance to the reader who's in on the secret of his feelings for her.
