I think the fact that Agatha can’t face Nicholas means there is still something extra that needs to be resolved. Billy says “is this what you did to Nicholas Scratch” and while the answer is clearly “no” it clearly still hits Agatha.

I think Rio and Agatha still have a deal or understanding or something. It’s clear they had a relationship. However Agatha had a child which requires a third party (or magic, since “from scratch”). There is something untold between Agatha and Rio.

I think Agatha did A LOT for Nicholas, but she wasn’t willing to give her own life, something she did do for Billy. So that is what she still has to face.