IMO Sir Walter is skin deep. Just as he went on and on about all "the many very plain faces he was continually passing in the streets" and the "dreadful multitude of ugly women in Bath; and as for the men! they were infinitely worse" (ch 15), I think that Sir Walter also had no problem pointing out the beautiful and handsome, and at that point complimenting on Anne's improved features, probably about the only things he noticed about his daughter.

So I'm not sure if Sir Walter had changed since he had been in Bath. I think that it was his nature to comment on anything skin deep, whether good or bad.

But I absolutely agree that Anne had changed. Not only in her "Elliot countenance" if that can be applied to her, but also in her outlook on life. I wonder if the episode with CW in Lyme had been some sort of a closure for her, her own way of "releasing" him and freeing herself from 8 years of pain. It was as if she could finally say, "I'm going to be OK."