I know we joke about progress, but if this actually is her admitting she likes him in a romantic sense then it’s about damn time. Took way too long.
She probably has had some sense of feelings for him for some time but couldn’t put words to those feelings. Or her question of why he is there when she is so hopeless is the whole reason she never let herself get those feelings out orreally act on them. She was afraid that he wouldn’t be cool with a girl who is like her where she shows one way at work and another in her personal life. Him saying those words to her just now are what finally made her realize he sees her for who she really is and he cares regardless.
Or the author really liked blueballing us and finally got told by their editor that they had to make SOME progress.