If they believed her they would have checked off for rape. So they obviously didn't believe her.
That's not true.
They didn't believe it enough.
I don't know why this simple concept is difficult for you.
Now why would they have believed her story about using fingers and not his penis?
They may not have.
They believed he used
something.
They couldn't be sure whether it was fingers or penis.
So they picked the one they were sure he committed.
Since the only thing that qualified for rape in New York was penis in vagina, they - quite correctly - didn't mark that as a yes.
None of that means they think she lied.
Now, it is quite possible that after-jury interviews have them saying "We think she lied about the penis thing", but you never bothered to argue that.
You keep insisting not checking the box means they think she lied, which is just logically incoherent.