"Her form, though not so correct as her sister's, in having the advantage of height, was more striking;"

By the comma logic you describe, then, if the comma after the word sister's was not there, that would be one continuous thought.

As in:

"Her form, though not so correct as her sister's in having the advantage of height, was more striking;"

The comma there separates the height from the sister's (Elinor's). Also, as I have already said, Jane Austen indicates that she is equating height and having a striking figure.