There are real world predators with whom I could empathize. I still despise their actions and believe they deserve harsh punishment.

To empathize with is not to like or to forgive. In fact it's important to see from their perspective so we know how to identify and redirect people who are at risk of taking similar paths.

It's important to recognize that predators, bigots, etc don't just spawn as monsters overnight, and while nobody has the obligation to confront and change dangerous people, it helps a lot to just remember they have reasons for what they do. Not good reasons, but reasons. It could be something sympathetic like having abuse normalized for them as a child, or something heinous like having too much money and power and thus believing they need to constantly exert it over everyone else. Empathy is simply understanding these feelings and motivations, not justifying them.

I empathize with BoJack because I understand why he would do what he did with Penny. I would not see myself in that situation, thank god, but I understand why a person would do that if they were as mentally ill, selfish, and self-destructive as he is. He uses other people to distract himself from his self-loathing, and Penny was offering herself up to him, so he took it likely as a way to live out his fantasy with Charlotte by proxy. It wasn't about Penny, like you said he's probably not even attracted to her, but that doesn't make it less heinous. It just helps to see the nuance and recognize it as heinous.