...he seems to think that Catherine is ignorant, but not stupid. Since she wants information, Henry gives it to her; but he leaves Catherine to draw her own conclusions about Isabella. That's probably a very liberal approach for a man of Henry's time.

In going from "Would he thank you, either on his own account or Miss Thorpe’s, for supposing that her affection, or at least her good behaviour, is only to be secured by her seeing nothing of Captain Tilney? Is he safe only in solitude?" to "Frederick ... will probably remain but a very short time..., Henry is going from trying to make a general point with Catherine to dealing with the (apparent) specific source of her unease. That does not strike me so much as contradictory as adapting to the specifics of the argument.