Interesting question.

I think this kind of applies to Wolfgang Grimmer from the manga Monster, as he was a child tortured by 511 Kinderheim, a torture bootcamp for children to find the next Hitler, where he was rendered someone who struggled to feel deep emotion for any bad event, but he still remained a good person helping whoever he could, similar to the main protagonist Tenma. I think this also applies to Android 16 from Dragon Ball Z, who was programmed to kill, but went against his programming due to his love of nature.

I don't share the idea that a lack of empathy immediately makes a character villainous.

Isaac Westcott is completely sane, and he's an extremely deplorable PE villain.

Yup, it mainly depends on their intentions and their actions, and if it lines up with what is conventionally considered morally good.

Exactly, "actions speak louder", and I think it would be quite fascinating to have more completely good characters who don't tend to be affected by the suffering of others, but strive to do good for altruistic reasons.