Quote

"It must be very agreeable to her to be settled within so easy a distance of her own family and friends."

"An easy distance, do you call it? It is nearly fifty miles."

"And what is fifty miles of good road? Little more than half a day's journey. Yes, I call it a very easy distance."

"I should never have considered the distance as one of the advantages of the match," cried Elizabeth. "I should never have said Mrs. Collins was settled near her family."

"It is a proof of your own attachment to Hertfordshire. anything beyond the very neighbourhood of Longbourn, I suppose, would appear far."

As he spoke there was a sort of smile which Elizabeth fancied she understood; he must be supposing her to be thinking of Jane and Netherfield, and she blushed as she answered --

"I do not mean to say that a woman may not be settled too near her family. The far and the near must be relative, and depend on many varying circumstances. Where there is fortune to make the expence of travelling unimportant, distance becomes no evil. But that is not the case here. Mr. and Mrs. Collins have a comfortable income, but not such a one as will allow of frequent journeys -- and I am persuaded my friend would not call herself near her family under less than half the present distance."

Mr. Darcy drew his chair a little towards her, and said, "You cannot have a right to such very strong local attachment. You cannot have been always at Longbourn."

I quoted the entire passage to highlight more of the context. When E says Charlotte isn't near [enough] to her family, he tries to explain it away with her own attachment to her home (perhaps it's the first time he considers that if he marries her, he will take her away from her beloved home - but doesn't think it a serious impediment, so he smiles). I admit I have no idea where Elizabeth gets the idea of him referring to Jane and Netherfield but this is why she considers a woman too near to her native family (because of the embarrassing presence of the Bennets) - yet, she answers with a negative/contradicting statement, giving Darcy hope that he's right, she thinks that being far from her family would be a good thing. Elizabeth then brings up financial considerations (to steer back the conversation to the Collinses), which Darcy, given that he thinks of himself and Elizabeth, may interpret as E knowing that she herself will not have this problem since they will be rich enough to travel, as well as an affirmation that E thinks Ch does feel far removed from her family/ misses them. I think Darcy's answer (that E surely isn't so much attached to Longbourn) means 1. that he hopes/thinks E has more experience from outside Longbourn (based on her intelligence/education as others said) so she won't feel out of her element when moves away from her childhood home; and 2. that she will not wish for so much contact with her family that would necessitate frequent travels. I'm sure this is speculation, but I feel not without grounds given the many layers of potential misunderstanding between them.

On another note, however, although I am not a native English speaker, so correct me if I'm wrong, but the way I learned traditional English grammar it requires more than a question mark to create a question: word order needs to be changed as well. "You can't have always been at Longbourn?" is not a grammatically correct question, only modern informal speech makes it acceptable. "You can't have been always at Longbourn, can you?" or "Can you have been always at Longbourn?" are questions. So I don't think JA made a mistake of confusing question mark/period.