I agree Fanny’s position seems unaccountable to Sir Thomas because he has an incomplete and inaccurate view of Fanny & Henry.

From his point of view Fanny ‘always received them [Henry’s attentions] very properly’ and he ‘never perceived them to be unpleasant’ or unwanted. I feel her modesty and indifference to Henry gave the impression of a very proper demeanor towards a gentleman who has not yet declared his intentions.

Also Henry told Sir Thomas that Fanny encouraged him when he proposed which I think was very unfair to Fanny. He was rejected and ought to have left Fanny alone.

From Sir Thomas’ point of view Henry’s affection for Fanny is obvious and what better talisman for his future care of Fanny. Henry’s behavior has not only been exemplary but he has shown a generous regard for the welfare of his future brother. His efforts to promote William are exactly the endeavor to prove his worth to a man who consistently promotes the well being of his extended family.