It seems petty straightforward to me why you'd be upset. By consistently comparing you to her and asking you to be more like her he's been sending the message "I like her better than you"... even if he might not really feel that way and was just being thoughtless, he was still definitely sending that message.
But that can be overlooked if there's no chance for them to have a relationship, if she doesn't like him back. No real need top worry about it because it's just a fantasy of his. However, now that she does like him back again, the obvious question is -- does he, in fact, like her better than you, and will he, therefore, prioritize her over you, thus slowly dismantling the trust and love in your relationship?
This may seem like a harsh way to look at it, but that'show I would interpret your fear, and that's why all of my suggested requests to him focused on him a) ceasing those negative messages to you, and b) treating you as special and important so that the trust and love can remain in your relationship.
The major players. Me, 30ish bi female. Gia, girlfriend of 4+ years. Clay, boyfriend/dom. Davis, ex/friend/"it's complicated." Eddie, roommate & fwb.
The supporting cast. Eric, Gia's husband. Bee, Gia and Eric's toddler. Dexter, Gia's lover. Helen, Eric's lover. Izzy and Nikki, Clay's partners. Liam, Eddie's husband.